data_9NDI # _entry.id 9NDI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.403 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9NDI pdb_00009ndi 10.2210/pdb9ndi/pdb WWPDB D_1000293139 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2025-04-09 _pdbx_audit_revision_history.part_number ? # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9NDI _pdbx_database_status.recvd_initial_deposition_date 2025-02-18 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email rs17@nyu.edu _pdbx_contact_author.name_first Ruojie _pdbx_contact_author.name_last Sha _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-0807-734X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Horvath, A.' 1 0009-0008-5770-8014 'Vecchioni, S.' 2 0000-0001-8243-650X 'Woloszyn, K.' 3 0000-0003-1200-583X 'Ohayon, Y.P.' 4 0000-0001-7500-4282 'Sha, R.' 5 0000-0002-0807-734X # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Shifted tensegrity triangles' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Horvath, A.' 1 0009-0008-5770-8014 primary 'Vecchioni, S.' 2 0000-0001-8243-650X primary 'Woloszyn, K.' 3 0000-0003-1200-583X primary 'Ohayon, Y.P.' 4 0000-0001-7500-4282 primary 'Sha, R.' 5 0000-0002-0807-734X # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*GP*CP*GP*TP*CP*A)-3') ; 3985.613 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3') ; 2371.582 1 ? ? ? ? 3 polymer syn ;DNA (5'-D(P*CP*T*GP*AP*CP*GP*CP*TP*GP*TP*GP*CP*T)-3') ; 3958.571 1 ? ? ? ? 4 polymer syn ;DNA (5'-D(P*GP*AP*GP*CP*TP*GP*TP*G)-3') ; 2482.640 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DA)(DC)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DT)(DC)(DA)' ACGGACAGCGTCA A ? 2 polydeoxyribonucleotide no no '(DC)(DA)(DC)(DA)(DC)(DC)(DG)(DT)' CACACCGT B ? 3 polydeoxyribonucleotide no no '(DC)(DT)(DG)(DA)(DC)(DG)(DC)(DT)(DG)(DT)(DG)(DC)(DT)' CTGACGCTGTGCT D ? 4 polydeoxyribonucleotide no no '(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DG)' GAGCTGTG X ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DA n 1 6 DC n 1 7 DA n 1 8 DG n 1 9 DC n 1 10 DG n 1 11 DT n 1 12 DC n 1 13 DA n 2 1 DC n 2 2 DA n 2 3 DC n 2 4 DA n 2 5 DC n 2 6 DC n 2 7 DG n 2 8 DT n 3 1 DC n 3 2 DT n 3 3 DG n 3 4 DA n 3 5 DC n 3 6 DG n 3 7 DC n 3 8 DT n 3 9 DG n 3 10 DT n 3 11 DG n 3 12 DC n 3 13 DT n 4 1 DG n 4 2 DA n 4 3 DG n 4 4 DC n 4 5 DT n 4 6 DG n 4 7 DT n 4 8 DG n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 13 'synthetic construct' ? 32630 ? 2 1 sample 1 8 'synthetic construct' ? 32630 ? 3 1 sample 1 13 'synthetic construct' ? 32630 ? 4 1 sample 1 8 'synthetic construct' ? 32630 ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DA 1 112 112 DA DA A . n A 1 2 DC 2 113 113 DC DC A . n A 1 3 DG 3 114 114 DG DG A . n A 1 4 DG 4 115 115 DG DG A . n A 1 5 DA 5 116 116 DA DA A . n A 1 6 DC 6 117 117 DC DC A . n A 1 7 DA 7 118 118 DA DA A . n A 1 8 DG 8 119 119 DG DG A . n A 1 9 DC 9 120 120 DC DC A . n A 1 10 DG 10 121 121 DG DG A . n A 1 11 DT 11 122 122 DT DT A . n A 1 12 DC 12 123 123 DC DC A . n A 1 13 DA 13 124 124 DA DA A . n B 2 1 DC 1 131 131 DC DC B . n B 2 2 DA 2 132 132 DA DA B . n B 2 3 DC 3 133 133 DC DC B . n B 2 4 DA 4 134 134 DA DA B . n B 2 5 DC 5 135 135 DC DC B . n B 2 6 DC 6 136 136 DC DC B . n B 2 7 DG 7 137 137 DG DG B . n B 2 8 DT 8 138 138 DT DT B . n C 3 1 DC 1 199 199 DC DC D . n C 3 2 DT 2 200 200 DT DT D . n C 3 3 DG 3 201 201 DG DG D . n C 3 4 DA 4 202 202 DA DA D . n C 3 5 DC 5 203 203 DC DC D . n C 3 6 DG 6 204 204 DG DG D . n C 3 7 DC 7 205 205 DC DC D . n C 3 8 DT 8 206 206 DT DT D . n C 3 9 DG 9 207 207 DG DG D . n C 3 10 DT 10 208 208 DT DT D . n C 3 11 DG 11 209 209 DG DG D . n C 3 12 DC 12 210 210 DC DC D . n C 3 13 DT 13 211 211 DT DT D . n D 4 1 DG 1 104 104 DG DG X . n D 4 2 DA 2 105 105 DA DA X . n D 4 3 DG 3 106 106 DG DG X . n D 4 4 DC 4 107 107 DC DC X . n D 4 5 DT 5 108 108 DT DT X . n D 4 6 DG 6 109 109 DG DG X . n D 4 7 DT 7 110 110 DT DT X . n D 4 8 DG 8 111 111 DG DG X . n # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? STARANISO ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 9NDI _cell.details ? _cell.formula_units_Z ? _cell.length_a 133.081 _cell.length_a_esd ? _cell.length_b 133.081 _cell.length_b_esd ? _cell.length_c 49.815 _cell.length_c_esd ? _cell.volume 764051.931 _cell.volume_esd ? _cell.Z_PDB 6 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9NDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall 'P 6c' _symmetry.space_group_name_H-M 'P 63' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9NDI _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details '338-293 at 0.4/hr' _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '100 mM MOPS, 1.25 M magnesium sulfate' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 9M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2023-03-19 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.991870 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 17-ID' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.991870 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 17-ID _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 403.04 _reflns.entry_id 9NDI _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 6.39 _reflns.d_resolution_low 19.96 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 968 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 90.6 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 19.5 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 6.9 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half .992 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 6.393 7.109 ? ? ? ? ? ? 194 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 .046 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 10.939 19.956 ? ? ? ? ? ? 194 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 .991 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 491.92 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9NDI _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 6.39 _refine.ls_d_res_low 19.96 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 965 _refine.ls_number_reflns_R_free 66 _refine.ls_number_reflns_R_work 899 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 90.02 _refine.ls_percent_reflns_R_free 6.84 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1619 _refine.ls_R_factor_R_free 0.1673 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1612 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.34 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 27.4633 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.7334 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 6.39 _refine_hist.d_res_low 19.96 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 861 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 861 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0082 ? 962 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.9021 ? 1475 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0526 ? 168 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0060 ? 42 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 40.0214 ? 408 ? f_dihedral_angle_d ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 6.39 _refine_ls_shell.d_res_low 19.96 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 66 _refine_ls_shell.number_reflns_R_work 899 _refine_ls_shell.percent_reflns_obs 90.02 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.1612 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.correlation_coeff_Fo_to_Fc ? _refine_ls_shell.correlation_coeff_Fo_to_Fc_free ? _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work ? _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free ? _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? _refine_ls_shell.R_factor_R_free 0.1673 # _struct.entry_id 9NDI _struct.title ;[3,8,9,P-1] Shifted tensegrity triangle with an (arm,center,arm) distribution of (3,8,9) base pairs, 1 nt sticky ends, and 5' phosphates ; _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9NDI _struct_keywords.text 'tensegrity triangle, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 9NDI 9NDI ? 1 ? 1 2 PDB 9NDI 9NDI ? 2 ? 1 3 PDB 9NDI 9NDI ? 3 ? 1 4 PDB 9NDI 9NDI ? 4 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 9NDI A 1 ? 13 ? 9NDI 112 ? 124 ? 112 124 2 2 9NDI B 1 ? 8 ? 9NDI 131 ? 138 ? 131 138 3 3 9NDI D 1 ? 13 ? 9NDI 199 ? 211 ? 199 211 4 4 9NDI X 1 ? 8 ? 9NDI 104 ? 111 ? 104 111 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D 1 2 A,B,C,D 1 3 A,B,C,D # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'native gel electrophoresis' _pdbx_struct_assembly_auth_evidence.details ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5000000000 -0.8660254038 0.0000000000 -66.5405000000 0.8660254038 -0.5000000000 0.0000000000 115.2515267610 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5000000000 0.8660254038 0.0000000000 -133.0810000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 112 B DT 138 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 112 B DT 138 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 113 B DG 137 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 113 B DG 137 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 113 B DG 137 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 114 B DC 136 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog7 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DG 7 N1 ? ? A DG 114 B DG 137 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 115 B DC 136 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 115 B DC 136 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 115 B DC 136 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 6 N3 ? ? ? 1_555 C DG 9 N1 ? ? A DC 117 D DG 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 6 N4 ? ? ? 1_555 C DG 9 O6 ? ? A DC 117 D DG 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 O2 ? ? ? 1_555 C DG 9 N2 ? ? A DC 117 D DG 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 7 N1 ? ? ? 1_555 C DT 8 N3 ? ? A DA 118 D DT 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 7 N6 ? ? ? 1_555 C DT 8 O4 ? ? A DA 118 D DT 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 8 N1 ? ? ? 1_555 C DC 7 N3 ? ? A DG 119 D DC 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 8 N2 ? ? ? 1_555 C DC 7 O2 ? ? A DG 119 D DC 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 8 O6 ? ? ? 1_555 C DC 7 N4 ? ? A DG 119 D DC 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N3 ? ? ? 1_555 C DG 6 N1 ? ? A DC 120 D DG 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 N4 ? ? ? 1_555 C DG 6 O6 ? ? A DC 120 D DG 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 O2 ? ? ? 1_555 C DG 6 N2 ? ? A DC 120 D DG 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 N1 ? ? ? 1_555 C DC 5 N3 ? ? A DG 121 D DC 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N2 ? ? ? 1_555 C DC 5 O2 ? ? A DG 121 D DC 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 O6 ? ? ? 1_555 C DC 5 N4 ? ? A DG 121 D DC 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 11 N3 ? ? ? 1_555 C DA 4 N1 ? ? A DT 122 D DA 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 11 O4 ? ? ? 1_555 C DA 4 N6 ? ? A DT 122 D DA 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 12 N3 ? ? ? 1_555 C DG 3 N2 ? ? A DC 123 D DG 201 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog28 hydrog ? ? A DC 12 N4 ? ? ? 1_555 C DA 4 N1 ? ? A DC 123 D DA 202 1_555 ? ? ? ? ? ? 'DC-DA MISPAIR' ? ? ? hydrog29 hydrog ? ? A DA 13 N1 ? ? ? 1_555 C DT 2 N3 ? ? A DA 124 D DT 200 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DA 13 N6 ? ? ? 1_555 C DT 2 O4 ? ? A DA 124 D DT 200 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B DC 1 N3 ? ? ? 1_555 D DG 8 N1 ? ? B DC 131 X DG 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B DC 1 N4 ? ? ? 1_555 D DG 8 O6 ? ? B DC 131 X DG 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B DC 1 O2 ? ? ? 1_555 D DG 8 N2 ? ? B DC 131 X DG 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B DA 2 N1 ? ? ? 1_555 D DT 7 N3 ? ? B DA 132 X DT 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B DA 2 N6 ? ? ? 1_555 D DT 7 O4 ? ? B DA 132 X DT 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B DC 3 N3 ? ? ? 1_555 D DG 6 N1 ? ? B DC 133 X DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B DC 3 N4 ? ? ? 1_555 D DG 6 O6 ? ? B DC 133 X DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B DC 3 O2 ? ? ? 1_555 D DG 6 N2 ? ? B DC 133 X DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B DA 4 N1 ? ? ? 1_555 D DT 5 N3 ? ? B DA 134 X DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B DA 4 N6 ? ? ? 1_555 D DT 5 O4 ? ? B DA 134 X DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C DG 11 N1 ? ? ? 1_555 D DC 4 N3 ? ? D DG 209 X DC 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C DG 11 N2 ? ? ? 1_555 D DC 4 O2 ? ? D DG 209 X DC 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C DG 11 O6 ? ? ? 1_555 D DC 4 N4 ? ? D DG 209 X DC 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C DC 12 N3 ? ? ? 1_555 D DG 3 N1 ? ? D DC 210 X DG 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C DC 12 N4 ? ? ? 1_555 D DG 3 O6 ? ? D DC 210 X DG 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C DC 12 O2 ? ? ? 1_555 D DG 3 N2 ? ? D DC 210 X DG 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C DT 13 N3 ? ? ? 1_555 D DA 2 N1 ? ? D DT 211 X DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C DT 13 O4 ? ? ? 1_555 D DA 2 N6 ? ? D DT 211 X DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_entry_details.entry_id 9NDI _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DA 112 ? ? "C1'" A DA 112 ? ? N9 A DA 112 ? ? 110.22 108.30 1.92 0.30 N 2 1 "O4'" D DT 206 ? ? "C1'" D DT 206 ? ? N1 D DT 206 ? ? 110.31 108.30 2.01 0.30 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 x-y,x,z+1/2 3 y,-x+y,z+1/2 4 -y,x-y,z 5 -x+y,-x,z 6 -x,-y,z+1/2 # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined -59.9941128549 14.5084688236 6.28248698313 7.21150389525 ? -0.412491825517 ? -2.38239815373 ? 4.34392040242 ? 1.55363607706 ? 3.78583462461 ? 6.57056188735 ? -4.25060358305 ? -7.45097590553 ? 8.18530172175 ? 2.82129524427 ? 7.38235754 ? -1.84774394167 ? 1.83908545165 ? -2.97705579355 ? -5.31353531357 ? -3.79262393877 ? 4.30791037263 ? -5.79070720623 ? 4.01570525042 ? 3.6818241959 ? 2 'X-RAY DIFFRACTION' ? refined -63.4894664345 24.6552558967 14.5797688061 9.00309603301 ? 0.282597123725 ? -1.23637936941 ? 2.77991735971 ? 0.273019437196 ? 5.63297938141 ? 1.99436062151 ? -0.634071301428 ? 5.84120498275 ? 2.67475256753 ? -0.289735880054 ? 4.15154605672 ? 1.58278058424 ? -0.609566148355 ? -5.65907891598 ? -0.778334960286 ? 2.12472619055 ? 2.97205869194 ? -3.6226641803 ? -1.25602638859 ? -3.81987381848 ? 3 'X-RAY DIFFRACTION' ? refined -62.6217081311 9.26244550654 8.78149748386 6.7380477804 ? -0.655608615835 ? -0.191639590471 ? 3.00549377418 ? -4.04488127616 ? 3.60942379123 ? 5.23585819932 ? -3.26916765945 ? 3.71429854201 ? 3.70305453692 ? -3.27174583051 ? 3.34922086463 ? 6.06482222862 ? -2.10446171346 ? -1.24893965962 ? -5.65779131883 ? -8.68548851535 ? 0.462812817124 ? -2.53734777835 ? -0.946344460369 ? -3.43753007705 ? 4 'X-RAY DIFFRACTION' ? refined -75.3491762808 20.7785906582 21.3522083024 8.03680266451 ? -0.294533762565 ? -5.24148413213 ? 5.36244397663 ? -0.107110414115 ? 7.05268824065 ? 2.09611532272 ? 8.3793884514 ? 2.0175301752 ? 4.16991329771 ? -6.34373487354 ? 8.577237674 ? 10.6363687603 ? -2.85566653006 ? 1.26821079287 ? 6.10227845902 ? 0.453349248264 ? 2.51563973017 ? 6.12735805176 ? -0.165673890481 ? 2.24973860769 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_PDB_ins_code _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 A ? A 112 ? A ? A 124 ? ? ;chain 'A' and (resid 112 through 124 ) ; 2 'X-RAY DIFFRACTION' 2 B ? B 131 ? B ? B 138 ? ? ;chain 'B' and (resid 131 through 138 ) ; 3 'X-RAY DIFFRACTION' 3 C ? D 199 ? C ? D 211 ? ? ;chain 'D' and (resid 199 through 211 ) ; 4 'X-RAY DIFFRACTION' 4 D ? X 104 ? D ? X 111 ? ? ;chain 'X' and (resid 104 through 111 ) ; # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9NDI 'double helix' 9NDI 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DA 1 1_555 B DT 8 1_555 0.183 -0.246 -0.936 -0.603 2.080 -0.986 1 A_DA112:DT138_B A 112 ? B 138 ? 20 1 1 A DC 2 1_555 B DG 7 1_555 0.192 -0.272 -0.750 0.863 -1.148 -1.203 2 A_DC113:DG137_B A 113 ? B 137 ? 19 1 1 A DG 4 1_555 B DC 6 1_555 -0.011 -0.503 1.729 11.509 1.134 1.360 3 A_DG115:DC136_B A 115 ? B 136 ? 19 1 1 A DC 6 1_555 C DG 9 1_555 0.048 -0.243 1.028 -2.244 -15.574 -5.530 4 A_DC117:DG207_D A 117 ? D 207 ? 19 1 1 A DA 7 1_555 C DT 8 1_555 0.270 -0.141 0.790 -2.995 -7.467 -1.715 5 A_DA118:DT206_D A 118 ? D 206 ? 20 1 1 A DG 8 1_555 C DC 7 1_555 -0.160 -0.053 0.155 -4.361 -4.189 3.158 6 A_DG119:DC205_D A 119 ? D 205 ? 19 1 1 A DC 9 1_555 C DG 6 1_555 0.131 -0.023 0.277 -0.226 3.851 1.108 7 A_DC120:DG204_D A 120 ? D 204 ? 19 1 1 A DG 10 1_555 C DC 5 1_555 -0.349 -0.186 -0.060 -5.647 -15.895 3.687 8 A_DG121:DC203_D A 121 ? D 203 ? 19 1 1 A DT 11 1_555 C DA 4 1_555 -0.053 -0.172 -0.481 2.409 -10.696 10.117 9 A_DT122:DA202_D A 122 ? D 202 ? 20 1 1 A DC 12 1_555 C DG 3 1_555 -1.573 0.298 -0.995 21.448 -7.479 15.077 10 A_DC123:DG201_D A 123 ? D 201 ? ? 1 1 A DA 13 1_555 C DT 2 1_555 -0.466 0.194 -1.219 17.918 -14.800 1.615 11 A_DA124:DT200_D A 124 ? D 200 ? 20 1 1 B DC 1 1_555 D DG 8 1_555 0.119 -0.124 -0.078 -2.940 -7.204 -3.249 12 B_DC131:DG111_X B 131 ? X 111 ? 19 1 1 B DA 2 1_555 D DT 7 1_555 0.116 -0.043 -0.209 -5.691 1.551 -1.460 13 B_DA132:DT110_X B 132 ? X 110 ? 20 1 1 B DC 3 1_555 D DG 6 1_555 0.255 -0.192 0.610 4.829 -0.921 0.425 14 B_DC133:DG109_X B 133 ? X 109 ? 19 1 1 B DA 4 1_555 D DT 5 1_555 -0.039 -0.054 -0.538 -21.377 -16.762 -3.690 15 B_DA134:DT108_X B 134 ? X 108 ? 20 1 1 C DG 11 1_555 D DC 4 1_555 -0.102 -0.324 -1.439 -16.527 -4.468 2.317 16 D_DG209:DC107_X D 209 ? X 107 ? 19 1 1 C DC 12 1_555 D DG 3 1_555 0.254 -0.428 -1.062 -6.257 -1.817 5.114 17 D_DC210:DG106_X D 210 ? X 106 ? 19 1 1 C DT 13 1_555 D DA 2 1_555 -0.189 -0.262 0.166 -1.956 -5.755 -1.602 18 D_DT211:DA105_X D 211 ? X 105 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DA 1 1_555 B DT 8 1_555 A DC 2 1_555 B DG 7 1_555 0.211 -1.131 3.206 -1.869 2.283 31.696 -2.466 -0.715 3.102 4.169 3.412 31.829 1 AA_DA112DC113:DG137DT138_BB A 112 ? B 138 ? A 113 ? B 137 ? 1 A DC 2 1_555 B DG 7 1_555 A DG 4 1_555 B DC 6 1_555 0.035 0.717 4.682 11.757 6.927 43.278 0.035 1.477 4.598 9.125 -15.488 45.279 2 AA_DC113DG115:DC136DG137_BB A 113 ? B 137 ? A 115 ? B 136 ? 1 A DC 6 1_555 C DG 9 1_555 A DA 7 1_555 C DT 8 1_555 -0.104 -0.025 3.181 4.875 1.405 35.440 -0.237 0.850 3.136 2.294 -7.957 35.789 3 AA_DC117DA118:DT206DG207_DD A 117 ? D 207 ? A 118 ? D 206 ? 1 A DA 7 1_555 C DT 8 1_555 A DG 8 1_555 C DC 7 1_555 -0.273 0.318 3.366 -3.083 -1.066 33.517 0.728 -0.046 3.366 -1.844 5.329 33.671 4 AA_DA118DG119:DC205DT206_DD A 118 ? D 206 ? A 119 ? D 205 ? 1 A DG 8 1_555 C DC 7 1_555 A DC 9 1_555 C DG 6 1_555 -0.776 -0.604 3.142 -2.065 3.863 29.404 -1.953 1.099 3.085 7.557 4.040 29.722 5 AA_DG119DC120:DG204DC205_DD A 119 ? D 205 ? A 120 ? D 204 ? 1 A DC 9 1_555 C DG 6 1_555 A DG 10 1_555 C DC 5 1_555 0.058 -0.698 2.892 2.078 17.400 31.585 -3.200 0.153 2.221 29.314 -3.501 36.012 6 AA_DC120DG121:DC203DG204_DD A 120 ? D 204 ? A 121 ? D 203 ? 1 A DG 10 1_555 C DC 5 1_555 A DT 11 1_555 C DA 4 1_555 -0.103 2.532 3.184 -0.850 2.241 41.695 3.318 0.055 3.311 3.145 1.193 41.760 7 AA_DG121DT122:DA202DC203_DD A 121 ? D 203 ? A 122 ? D 202 ? 1 A DT 11 1_555 C DA 4 1_555 A DC 12 1_555 C DG 3 1_555 -1.216 -0.158 2.678 -2.136 11.182 23.578 -2.861 2.208 2.450 25.544 4.878 26.147 8 AA_DT122DC123:DG201DA202_DD A 122 ? D 202 ? A 123 ? D 201 ? 1 A DC 12 1_555 C DG 3 1_555 A DA 13 1_555 C DT 2 1_555 -0.041 0.121 4.172 4.143 5.759 28.836 -1.314 1.196 4.074 11.348 -8.164 29.678 9 AA_DC123DA124:DT200DG201_DD A 123 ? D 201 ? A 124 ? D 200 ? 1 B DC 1 1_555 D DG 8 1_555 B DA 2 1_555 D DT 7 1_555 0.855 0.234 3.231 1.167 -6.709 30.565 1.683 -1.367 3.140 -12.532 -2.179 31.297 10 BB_DC131DA132:DT110DG111_XX B 131 ? X 111 ? B 132 ? X 110 ? 1 B DA 2 1_555 D DT 7 1_555 B DC 3 1_555 D DG 6 1_555 0.547 -0.795 3.035 -5.583 6.183 32.027 -2.329 -1.803 2.708 10.976 9.911 33.065 11 BB_DA132DC133:DG109DT110_XX B 132 ? X 110 ? B 133 ? X 109 ? 1 B DC 3 1_555 D DG 6 1_555 B DA 4 1_555 D DT 5 1_555 -0.452 -0.142 4.381 7.271 46.861 29.851 -3.923 1.070 2.246 58.906 -9.140 55.572 12 BB_DC133DA134:DT108DG109_XX B 133 ? X 109 ? B 134 ? X 108 ? 1 B DA 4 1_555 D DT 5 1_555 C DG 11 1_555 D DC 4 1_555 -0.348 0.424 3.368 1.129 0.852 38.851 0.531 0.664 3.365 1.280 -1.696 38.876 13 BD_DA134DG209:DC107DT108_XX B 134 ? X 108 ? D 209 ? X 107 ? 1 C DG 11 1_555 D DC 4 1_555 C DC 12 1_555 D DG 3 1_555 -1.004 -0.523 3.068 -8.980 4.707 35.725 -1.431 0.417 3.129 7.489 14.286 37.090 14 DD_DG209DC210:DG106DC107_XX D 209 ? X 107 ? D 210 ? X 106 ? 1 C DC 12 1_555 D DG 3 1_555 C DT 13 1_555 D DA 2 1_555 -0.612 -0.374 3.588 -10.626 4.145 33.872 -1.284 -0.726 3.546 6.877 17.630 35.688 15 DD_DC210DT211:DA105DG106_XX D 210 ? X 106 ? D 211 ? X 105 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Office of Naval Research (ONR)' 'United States' N000141912596 1 'Department of Energy (DOE, United States)' 'United States' DE-SC0007991 2 'National Science Foundation (NSF, United States)' 'United States' CCF-2106790 3 'National Science Foundation (NSF, United States)' 'United States' GCR-2317843 4 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 8D93 _pdbx_initial_refinement_model.details 'tensegrity triangle' # _space_group.name_H-M_alt 'P 63' _space_group.name_Hall 'P 6c' _space_group.IT_number 173 _space_group.crystal_system hexagonal _space_group.id 1 # _atom_sites.entry_id 9NDI _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.007514 _atom_sites.fract_transf_matrix[1][2] 0.004338 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.008677 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.020074 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 5.96793 ? ? ? 14.89577 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 6.96715 ? ? ? 11.43723 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 7.96527 ? ? ? 9.05267 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 14.90797 ? ? ? 11.91318 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ # loop_ #