data_5CNR # _entry.id 5CNR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 5CNR pdb_00005cnr 10.2210/pdb5cnr/pdb WWPDB D_1000211914 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details . _pdbx_database_related.db_id 4P97 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5CNR _pdbx_database_status.recvd_initial_deposition_date 2015-07-18 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Boerneke, M.' 1 'Dibrov, S.' 2 'Hermann, T.' 3 # _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 GE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_id_ASTM ACIEAY _citation.journal_id_CSD 0179 _citation.journal_id_ISSN 1521-3773 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 55 _citation.language ? _citation.page_first 4097 _citation.page_last 4100 _citation.title 'Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.' _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/anie.201600233 _citation.pdbx_database_id_PubMed 26914842 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Boerneke, M.A.' 1 ? primary 'Dibrov, S.M.' 2 ? primary 'Hermann, T.' 3 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 5CNR _cell.details ? _cell.formula_units_Z ? _cell.length_a 59.934 _cell.length_a_esd ? _cell.length_b 59.934 _cell.length_b_esd ? _cell.length_c 262.622 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 36 _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 ? # _symmetry.entry_id 5CNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? # 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 ;RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3') ; 4968.999 2 ? ? ? ? 2 polymer syn ;RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3') ; 3624.258 2 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 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 polyribonucleotide no no GUCUACCCACCUCGCC GUCUACCCACCUCGCC A,E ? 2 polyribonucleotide no no AGAGGACGGCG AGAGGACGGCG B,F ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 U n 1 3 C n 1 4 U n 1 5 A n 1 6 C n 1 7 C n 1 8 C n 1 9 A n 1 10 C n 1 11 C n 1 12 U n 1 13 C n 1 14 G n 1 15 C n 1 16 C n 2 1 A n 2 2 G n 2 3 A n 2 4 G n 2 5 G n 2 6 A n 2 7 C n 2 8 G n 2 9 G n 2 10 C n 2 11 G 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 16 'Seneca valley virus' ? 390157 ? 2 1 sample 1 11 'Seneca valley virus' ? 390157 ? # loop_ _struct_ref.db_code _struct_ref.db_name _struct_ref.details _struct_ref.entity_id _struct_ref.id _struct_ref.seq_align _struct_ref.seq_dif _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_align_end 5CNR PDB ? 1 1 ? ? 5CNR ? ? 1 ? 5CNR PDB ? 2 2 ? ? 5CNR ? ? 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 5CNR A 1 ? 16 ? 5CNR 3 ? 18 ? 3 18 2 2 5CNR B 1 ? 11 ? 5CNR 37 ? 47 ? 37 47 3 1 5CNR E 1 ? 16 ? 5CNR 3 ? 18 ? 3 18 4 2 5CNR F 1 ? 11 ? 5CNR 37 ? 47 ? 37 47 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _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 5CNR _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.64 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 53.42 _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_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 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 281 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;drop: 20% MPD, 55 mM NaCl, 12 mM spermine, 40 mM Tris well: 18% MPD, 120 mM NaCl ; _exptl_crystal_grow.pdbx_pH_range ? # _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_detector.details ? _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MAR scanner 345 mm plate' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-01-13 # _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 1.54 _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 'ROTATING ANODE' _diffrn_source.target ? _diffrn_source.type 'RIGAKU FR-D' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.54 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_synchrotron_site ? # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5CNR _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.59 _reflns.d_resolution_low 48.3 _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 5011 _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 83.2 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 17.6 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value 0.076 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 35.5 _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 ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.59 _reflns_shell.d_res_low 2.68 _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_all 11.7 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_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 2.0 _reflns_shell.pdbx_Rsym_value ? _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 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] -21.4768 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][2] -21.4768 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] -52.3477 _refine.B_iso_max ? _refine.B_iso_mean ? _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 5CNR _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 2.59 _refine.ls_d_res_low 19.403 _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 4985 _refine.ls_number_reflns_R_free 500 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 83.82 _refine.ls_percent_reflns_R_free 10.03 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1979 _refine.ls_R_factor_R_free 0.2444 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1925 _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 91.673 _refine.solvent_model_param_ksol 0.298 _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 1.35 _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 4P97 _refine.pdbx_stereochemistry_target_values ML _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 1.20 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.98 _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 33.86 _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 0.35 _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.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1136 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1137 _refine_hist.d_res_high 2.59 _refine_hist.d_res_low 19.403 # 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' ? 0.002 ? 1266 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.445 ? 1966 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 14.080 ? 632 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.051 ? 266 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.002 ? 54 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _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 _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _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_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.5963 2.8568 . . 53 474 36.00 . . . 0.4811 . 0.4279 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.8568 3.2685 . . 141 1271 98.00 . . . 0.4152 . 0.3209 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.2685 4.1116 . . 148 1338 100.00 . . . 0.2621 . 0.2473 . . . . . . . . . . 'X-RAY DIFFRACTION' 4.1116 19.4032 . . 158 1402 100.00 . . . 0.1986 . 0.1418 . . . . . . . . . . # _struct.entry_id 5CNR _struct.title 'Crystal structure-guided design of self-assembling RNA nano triangles' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5CNR _struct_keywords.text 'seneca valley virus, nanotriangle, self-assembly, RNA' _struct_keywords.pdbx_keywords RNA # 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 1 ? D N N 2 ? E N N 3 ? # 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 G 1 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 3 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 3 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 3 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 B A 6 N1 ? ? A U 4 B A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 B A 6 N6 ? ? A U 4 B A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 5 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 5 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 5 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 4 N3 ? ? ? 1_555 B A 3 N7 ? ? A U 6 B A 39 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog10 hydrog ? ? A U 4 O2 ? ? ? 1_555 B A 3 N6 ? ? A U 6 B A 39 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog11 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 12 B G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 12 B G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 12 B G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 13 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 13 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 13 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 1 N1 ? ? A U 14 B A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 1 N6 ? ? A U 14 B A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? C U 2 N3 ? ? ? 1_555 D A 6 N1 ? ? E U 4 F A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? C U 2 O4 ? ? ? 1_555 D A 6 N6 ? ? E U 4 F A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C C 3 N4 ? ? ? 1_555 D G 5 O6 ? ? E C 5 F G 41 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog22 hydrog ? ? C U 4 N3 ? ? ? 1_555 D A 3 N7 ? ? E U 6 F A 39 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog23 hydrog ? ? C U 4 O2 ? ? ? 1_555 D A 3 N6 ? ? E U 6 F A 39 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog24 hydrog ? ? C C 10 N4 ? ? ? 1_555 D G 4 O6 ? ? E C 12 F G 40 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog25 hydrog ? ? C C 11 N4 ? ? ? 1_555 D G 2 O6 ? ? E C 13 F G 38 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog26 hydrog ? ? C U 12 N3 ? ? ? 1_555 D A 1 N1 ? ? E U 14 F A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C U 12 O4 ? ? ? 1_555 D A 1 N6 ? ? E U 14 F A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 5CNR _atom_sites.fract_transf_matrix[1][1] 0.016685 _atom_sites.fract_transf_matrix[1][2] 0.009633 _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] 0.019266 _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] 0.003808 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CL N O P # 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 G 1 3 3 G G A . n A 1 2 U 2 4 4 U U A . n A 1 3 C 3 5 5 C C A . n A 1 4 U 4 6 6 U U A . n A 1 5 A 5 7 7 A A A . n A 1 6 C 6 8 8 C C A . n A 1 7 C 7 9 9 C C A . n A 1 8 C 8 10 10 C C A . n A 1 9 A 9 11 11 A A A . n A 1 10 C 10 12 12 C C A . n A 1 11 C 11 13 13 C C A . n A 1 12 U 12 14 14 U U A . n A 1 13 C 13 15 15 C C A . n A 1 14 G 14 16 16 G G A . n A 1 15 C 15 17 17 C C A . n A 1 16 C 16 18 18 C C A . n B 2 1 A 1 37 37 A A B . n B 2 2 G 2 38 38 G G B . n B 2 3 A 3 39 39 A A B . n B 2 4 G 4 40 40 G G B . n B 2 5 G 5 41 41 G G B . n B 2 6 A 6 42 42 A A B . n B 2 7 C 7 43 43 C C B . n B 2 8 G 8 44 44 G G B . n B 2 9 G 9 45 45 G G B . n B 2 10 C 10 46 46 C C B . n B 2 11 G 11 47 47 G G B . n C 1 1 G 1 3 3 G G E . n C 1 2 U 2 4 4 U U E . n C 1 3 C 3 5 5 C C E . n C 1 4 U 4 6 6 U U E . n C 1 5 A 5 7 7 A A E . n C 1 6 C 6 8 8 C C E . n C 1 7 C 7 9 9 C C E . n C 1 8 C 8 10 10 C C E . n C 1 9 A 9 11 11 A A E . n C 1 10 C 10 12 12 C C E . n C 1 11 C 11 13 13 C C E . n C 1 12 U 12 14 14 U U E . n C 1 13 C 13 15 15 C C E . n C 1 14 G 14 16 16 G G E . n C 1 15 C 15 17 17 C C E . n C 1 16 C 16 18 18 C C E . n D 2 1 A 1 37 37 A A F . n D 2 2 G 2 38 38 G G F . n D 2 3 A 3 39 39 A A F . n D 2 4 G 4 40 40 G G F . n D 2 5 G 5 41 41 G G F . n D 2 6 A 6 42 42 A A F . n D 2 7 C 7 43 43 C C F . n D 2 8 G 8 44 44 G G F . n D 2 9 G 9 45 45 G G F . n D 2 10 C 10 46 46 C C F . n D 2 11 G 11 47 47 G G F . n # _pdbx_nonpoly_scheme.asym_id E _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id CL _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id CL _pdbx_nonpoly_scheme.auth_mon_id CL _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.pdb_ins_code . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E 2 1 C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1170 ? 1 MORE -8 ? 1 'SSA (A^2)' 5340 ? 2 'ABSA (A^2)' 960 ? 2 MORE 0 ? 2 'SSA (A^2)' 5460 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2016-03-09 2 'Structure model' 1 1 2016-03-23 3 'Structure model' 1 2 2023-09-27 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' citation 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_initial_refinement_model 6 3 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_citation.journal_id_CSD' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' # 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' ? ? 48.0340 19.1910 314.9542 0.7332 ? 0.0774 ? 0.0538 ? 0.7677 ? -0.1790 ? 0.8781 ? 0.4743 ? -0.4892 ? 0.6273 ? 0.5750 ? -0.6049 ? 0.8175 ? -0.0690 ? 0.5182 ? 0.1884 ? -0.7570 ? -0.4073 ? -0.5960 ? 1.1167 ? 0.5105 ? 0.0012 ? 2 'X-RAY DIFFRACTION' ? ? 45.9397 1.1546 319.9836 0.7613 ? -0.0074 ? -0.0208 ? 0.5890 ? -0.0286 ? 0.7115 ? 0.1278 ? -0.2031 ? 0.0486 ? 0.4545 ? 0.0982 ? 0.2167 ? -0.2147 ? 0.8948 ? -0.1075 ? -0.1113 ? 0.1664 ? -0.6507 ? -0.1178 ? -0.6949 ? 0.0010 ? 3 'X-RAY DIFFRACTION' ? ? 51.1097 13.7150 315.6010 0.7170 ? -0.0497 ? 0.1197 ? 0.5672 ? -0.1061 ? 0.8007 ? 0.2425 ? 0.0993 ? 0.2936 ? 0.0589 ? 0.1816 ? 0.4860 ? -0.6757 ? 0.1955 ? 0.5104 ? -0.2893 ? 0.2143 ? -0.1226 ? 0.1176 ? -0.1109 ? 0.0006 ? 4 'X-RAY DIFFRACTION' ? ? 69.5436 19.8698 319.0855 0.6469 ? -0.0321 ? -0.0424 ? 0.9556 ? -0.0553 ? 1.0780 ? 0.5954 ? -0.2439 ? 0.3916 ? 0.9703 ? -0.6950 ? 0.5783 ? 0.0348 ? 0.9520 ? -1.1130 ? -0.3558 ? 0.8787 ? -0.0619 ? 0.5339 ? 0.4162 ? 0.0137 ? 5 'X-RAY DIFFRACTION' ? ? 70.3314 -10.4381 357.8871 1.7978 ? -0.0785 ? -0.4449 ? 2.0205 ? 0.2452 ? 0.7158 ? 5.4197 ? -0.6789 ? 0.2031 ? 0.7599 ? 0.4293 ? 0.3298 ? -0.4373 ? -0.9263 ? 0.0995 ? 1.4756 ? 0.4195 ? -0.5035 ? 1.3481 ? 0.1397 ? 0.6066 ? 6 'X-RAY DIFFRACTION' ? ? 78.5250 -24.8887 367.4228 1.0374 ? 0.0893 ? -0.2018 ? 1.4578 ? -0.1877 ? 0.7214 ? 0.0046 ? -0.0202 ? 0.0047 ? 0.0691 ? -0.0184 ? 0.0068 ? -0.0899 ? -0.2028 ? 0.5001 ? 0.8389 ? 0.7471 ? -1.0786 ? -0.6920 ? 0.3415 ? 0.0060 ? 7 'X-RAY DIFFRACTION' ? ? 75.3178 -10.7416 359.4929 1.3951 ? 0.1623 ? -0.4007 ? 1.9950 ? 0.0297 ? 0.6296 ? 3.7834 ? -1.0847 ? -1.6789 ? 0.3501 ? 0.4915 ? 0.7462 ? -0.9410 ? -0.4720 ? 0.0443 ? -0.5019 ? 0.0801 ? -0.1131 ? 0.3305 ? 0.4012 ? -1.5226 ? 8 'X-RAY DIFFRACTION' ? ? 87.2368 4.6765 362.7994 1.5402 ? -0.2033 ? -0.0188 ? 1.8470 ? 0.5361 ? 0.9612 ? 0.0750 ? -0.3101 ? -0.0932 ? 1.5418 ? 0.5262 ? 0.1853 ? 0.1724 ? -0.2893 ? -0.9052 ? 1.7091 ? 0.4424 ? -0.1736 ? 0.7103 ? 0.5820 ? 0.7082 ? # 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.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.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resseq 3:11) ; 2 'X-RAY DIFFRACTION' 2 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resseq 12:18) ; 3 'X-RAY DIFFRACTION' 3 ? ? ? ? ? ? ? ? ? ;chain 'B' and (resseq 37:42) ; 4 'X-RAY DIFFRACTION' 4 ? ? ? ? ? ? ? ? ? ;chain 'B' and (resseq 43:47) ; 5 'X-RAY DIFFRACTION' 5 ? ? ? ? ? ? ? ? ? ;chain 'E' and (resseq 3:13) ; 6 'X-RAY DIFFRACTION' 6 ? ? ? ? ? ? ? ? ? ;chain 'E' and (resseq 14:18) ; 7 'X-RAY DIFFRACTION' 7 ? ? ? ? ? ? ? ? ? ;chain 'F' and (resseq 37:42) ; 8 'X-RAY DIFFRACTION' 8 ? ? ? ? ? ? ? ? ? ;chain 'F' and (resseq 43:47) ; # 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 ? ? ? 1.7.3_928 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CL CL CL N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 U OP3 O N N 112 U P P N N 113 U OP1 O N N 114 U OP2 O N N 115 U "O5'" O N N 116 U "C5'" C N N 117 U "C4'" C N R 118 U "O4'" O N N 119 U "C3'" C N S 120 U "O3'" O N N 121 U "C2'" C N R 122 U "O2'" O N N 123 U "C1'" C N R 124 U N1 N N N 125 U C2 C N N 126 U O2 O N N 127 U N3 N N N 128 U C4 C N N 129 U O4 O N N 130 U C5 C N N 131 U C6 C N N 132 U HOP3 H N N 133 U HOP2 H N N 134 U "H5'" H N N 135 U "H5''" H N N 136 U "H4'" H N N 137 U "H3'" H N N 138 U "HO3'" H N N 139 U "H2'" H N N 140 U "HO2'" H N N 141 U "H1'" H N N 142 U H3 H N N 143 U H5 H N N 144 U H6 H N N 145 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5CNR 'double helix' 5CNR 'a-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 G 1 1_555 B C 7 1_555 0.439 -0.135 0.023 -3.906 -8.593 0.692 1 A_G3:C43_B A 3 ? B 43 ? 19 1 1 A U 2 1_555 B A 6 1_555 0.274 -0.106 -0.154 4.456 -11.958 -2.844 2 A_U4:A42_B A 4 ? B 42 ? 20 1 1 A C 3 1_555 B G 5 1_555 0.694 0.168 0.186 -3.929 -5.423 5.434 3 A_C5:G41_B A 5 ? B 41 ? 19 1 1 A U 4 1_555 B A 3 1_555 4.167 -2.161 0.494 -5.227 3.474 -92.074 4 A_U6:A39_B A 6 ? B 39 ? 24 4 1 A C 10 1_555 B G 4 1_555 0.188 -0.223 -1.058 22.228 -8.966 2.232 5 A_C12:G40_B A 12 ? B 40 ? 19 1 1 A C 11 1_555 B G 2 1_555 -0.067 -0.105 0.157 11.398 -15.094 -0.673 6 A_C13:G38_B A 13 ? B 38 ? 19 1 1 A U 12 1_555 B A 1 1_555 -0.110 -0.067 -0.033 12.118 -18.079 -4.912 7 A_U14:A37_B A 14 ? B 37 ? 20 1 1 C U 2 1_555 D A 6 1_555 -0.200 -0.035 -0.332 -0.162 -8.260 1.669 8 E_U4:A42_F E 4 ? F 42 ? 20 1 1 C C 3 1_555 D G 5 1_555 -0.481 -0.066 -1.065 5.524 -11.785 -9.403 9 E_C5:G41_F E 5 ? F 41 ? ? 1 1 C U 4 1_555 D A 3 1_555 4.256 -2.635 1.392 -4.656 20.378 -85.474 10 E_U6:A39_F E 6 ? F 39 ? 24 4 1 C C 10 1_555 D G 4 1_555 -0.395 0.680 -1.630 36.917 -6.308 -16.674 11 E_C12:G40_F E 12 ? F 40 ? ? ? 1 C C 11 1_555 D G 2 1_555 0.433 -0.204 -0.708 10.899 -14.185 -12.595 12 E_C13:G38_F E 13 ? F 38 ? ? 1 1 C U 12 1_555 D A 1 1_555 -0.655 -0.079 0.098 1.136 -12.010 -3.160 13 E_U14:A37_F E 14 ? F 37 ? 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 G 1 1_555 B C 7 1_555 A U 2 1_555 B A 6 1_555 -0.545 -1.594 3.036 -0.036 1.614 30.427 -3.328 1.031 2.950 3.072 0.069 30.468 1 AA_G3U4:A42C43_BB A 3 ? B 43 ? A 4 ? B 42 ? 1 A U 2 1_555 B A 6 1_555 A C 3 1_555 B G 5 1_555 0.685 -1.659 3.408 -0.174 6.303 34.320 -3.722 -1.168 3.061 10.571 0.292 34.877 2 AA_U4C5:G41A42_BB A 4 ? B 42 ? A 5 ? B 41 ? 1 A C 3 1_555 B G 5 1_555 A U 4 1_555 B A 3 1_555 -3.318 -1.833 3.293 1.971 1.612 71.551 -1.621 2.903 3.177 1.378 -1.685 71.591 3 AA_C5U6:A39G41_BB A 5 ? B 41 ? A 6 ? B 39 ? 1 A C 10 1_555 B G 4 1_555 A C 11 1_555 B G 2 1_555 1.861 -1.543 3.389 -6.559 10.509 53.926 -2.262 -2.381 2.839 11.419 7.127 55.226 4 AA_C12C13:G38G40_BB A 12 ? B 40 ? A 13 ? B 38 ? 1 A C 11 1_555 B G 2 1_555 A U 12 1_555 B A 1 1_555 -0.017 -1.603 3.239 0.088 5.603 36.569 -3.248 0.038 2.969 8.866 -0.139 36.982 5 AA_C13U14:A37G38_BB A 13 ? B 38 ? A 14 ? B 37 ? 1 C U 2 1_555 D A 6 1_555 C C 3 1_555 D G 5 1_555 0.030 -1.337 3.256 8.084 10.017 30.775 -3.899 1.211 2.630 17.924 -14.464 33.298 6 EE_U4C5:G41A42_FF E 4 ? F 42 ? E 5 ? F 41 ? 1 C C 3 1_555 D G 5 1_555 C U 4 1_555 D A 3 1_555 -2.233 -2.282 3.904 -7.016 13.557 84.179 -2.049 1.459 3.717 10.041 5.196 85.297 7 EE_C5U6:A39G41_FF E 5 ? F 41 ? E 6 ? F 39 ? 1 C C 10 1_555 D G 4 1_555 C C 11 1_555 D G 2 1_555 2.118 -1.988 3.661 -2.553 15.336 62.313 -2.567 -2.113 3.068 14.580 2.427 64.034 8 EE_C12C13:G38G40_FF E 12 ? F 40 ? E 13 ? F 38 ? 1 C C 11 1_555 D G 2 1_555 C U 12 1_555 D A 1 1_555 0.698 -2.117 3.508 -6.296 9.058 32.332 -5.003 -2.158 2.657 15.706 10.917 34.115 9 EE_C13U14:A37G38_FF E 13 ? F 38 ? E 14 ? F 37 ? # _pdbx_audit_support.funding_organization 'UCSD Academic Senate' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number RM069B _pdbx_audit_support.ordinal 1 # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 'CHLORIDE ION' _pdbx_entity_nonpoly.comp_id CL # _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 4P97 _pdbx_initial_refinement_model.details ? #