data_5DEK # _entry.id 5DEK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 5DEK pdb_00005dek 10.2210/pdb5dek/pdb WWPDB D_1000213094 ? ? # 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 2016-07-20 2 'Structure model' 1 1 2024-03-06 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' # 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 2 'Structure model' atom_type 2 2 'Structure model' chem_comp_atom 3 2 'Structure model' chem_comp_bond 4 2 'Structure model' database_2 5 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5DEK _pdbx_database_status.recvd_initial_deposition_date 2015-08-25 _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details . _pdbx_database_related.db_id 5DER _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Harp, J.M.' 1 'Egli, M.' 2 # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Org.Chem. _citation.journal_id_ASTM JOCEAH _citation.journal_id_CSD 0035 _citation.journal_id_ISSN 0022-3263 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 81 _citation.language ? _citation.page_first 2261 _citation.page_last 2279 _citation.title ;Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. ; _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.joc.5b02375 _citation.pdbx_database_id_PubMed 26940174 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kel In, A.V.' 1 ? primary 'Zlatev, I.' 2 ? primary 'Harp, J.' 3 ? primary 'Jayaraman, M.' 4 ? primary 'Bisbe, A.' 5 ? primary 'O Shea, J.' 6 ? primary 'Taneja, N.' 7 ? primary 'Manoharan, R.M.' 8 ? primary 'Khan, S.' 9 ? primary 'Charisse, K.' 10 ? primary 'Maier, M.A.' 11 ? primary 'Egli, M.' 12 ? primary 'Rajeev, K.G.' 13 ? primary 'Manoharan, M.' 14 ? # 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 oligonucleotide containing dT' 2524.588 4 ? ? ? ? 2 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 3 water nat water 18.015 66 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code 'CGAA(DT)UCG' _entity_poly.pdbx_seq_one_letter_code_can CGAATUCG _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT HEXAMMINE(III)' NCO 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 A n 1 4 A n 1 5 DT n 1 6 U n 1 7 C n 1 8 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 8 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 C 1 101 101 C C A . n A 1 2 G 2 102 102 G G A . n A 1 3 A 3 103 103 A A A . n A 1 4 A 4 104 104 A A A . n A 1 5 DT 5 105 105 DT DT A . n A 1 6 U 6 106 106 U U A . n A 1 7 C 7 107 107 C C A . n A 1 8 G 8 108 108 G G A . n B 1 1 C 1 209 209 C C B . n B 1 2 G 2 210 210 G G B . n B 1 3 A 3 211 211 A A B . n B 1 4 A 4 212 212 A A B . n B 1 5 DT 5 213 213 DT DT B . n B 1 6 U 6 214 214 U U B . n B 1 7 C 7 215 215 C C B . n B 1 8 G 8 216 216 G G B . n C 1 1 C 1 101 101 C C C . n C 1 2 G 2 102 102 G G C . n C 1 3 A 3 103 103 A A C . n C 1 4 A 4 104 104 A A C . n C 1 5 DT 5 105 105 DT DT C . n C 1 6 U 6 106 106 U U C . n C 1 7 C 7 107 107 C C C . n C 1 8 G 8 108 108 G G C . n D 1 1 C 1 209 209 C C D . n D 1 2 G 2 210 210 G G D . n D 1 3 A 3 211 211 A A D . n D 1 4 A 4 212 212 A A D . n D 1 5 DT 5 213 213 DT DT D . n D 1 6 U 6 214 214 U U D . n D 1 7 C 7 215 215 C C D . n D 1 8 G 8 216 216 G G D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 NCO 1 301 2 NCO NCO B . F 2 NCO 1 201 1 NCO NCO C . G 3 HOH 1 201 12 HOH HOH A . G 3 HOH 2 202 3 HOH HOH A . G 3 HOH 3 203 9 HOH HOH A . G 3 HOH 4 204 44 HOH HOH A . G 3 HOH 5 205 58 HOH HOH A . G 3 HOH 6 206 31 HOH HOH A . G 3 HOH 7 207 23 HOH HOH A . G 3 HOH 8 208 36 HOH HOH A . G 3 HOH 9 209 54 HOH HOH A . G 3 HOH 10 210 11 HOH HOH A . G 3 HOH 11 211 51 HOH HOH A . G 3 HOH 12 212 46 HOH HOH A . G 3 HOH 13 213 30 HOH HOH A . G 3 HOH 14 214 39 HOH HOH A . H 3 HOH 1 401 8 HOH HOH B . H 3 HOH 2 402 4 HOH HOH B . H 3 HOH 3 403 19 HOH HOH B . H 3 HOH 4 404 48 HOH HOH B . H 3 HOH 5 405 2 HOH HOH B . H 3 HOH 6 406 13 HOH HOH B . H 3 HOH 7 407 47 HOH HOH B . H 3 HOH 8 408 21 HOH HOH B . H 3 HOH 9 409 45 HOH HOH B . H 3 HOH 10 410 53 HOH HOH B . H 3 HOH 11 411 6 HOH HOH B . H 3 HOH 12 412 29 HOH HOH B . H 3 HOH 13 413 35 HOH HOH B . H 3 HOH 14 414 14 HOH HOH B . H 3 HOH 15 415 32 HOH HOH B . H 3 HOH 16 416 42 HOH HOH B . H 3 HOH 17 417 37 HOH HOH B . H 3 HOH 18 418 61 HOH HOH B . I 3 HOH 1 301 40 HOH HOH C . I 3 HOH 2 302 26 HOH HOH C . I 3 HOH 3 303 22 HOH HOH C . I 3 HOH 4 304 5 HOH HOH C . I 3 HOH 5 305 28 HOH HOH C . I 3 HOH 6 306 15 HOH HOH C . I 3 HOH 7 307 25 HOH HOH C . I 3 HOH 8 308 27 HOH HOH C . I 3 HOH 9 309 33 HOH HOH C . I 3 HOH 10 310 20 HOH HOH C . I 3 HOH 11 311 38 HOH HOH C . I 3 HOH 12 312 24 HOH HOH C . I 3 HOH 13 313 59 HOH HOH C . I 3 HOH 14 314 66 HOH HOH C . I 3 HOH 15 315 63 HOH HOH C . J 3 HOH 1 301 49 HOH HOH D . J 3 HOH 2 302 34 HOH HOH D . J 3 HOH 3 303 55 HOH HOH D . J 3 HOH 4 304 60 HOH HOH D . J 3 HOH 5 305 56 HOH HOH D . J 3 HOH 6 306 1 HOH HOH D . J 3 HOH 7 307 17 HOH HOH D . J 3 HOH 8 308 18 HOH HOH D . J 3 HOH 9 309 16 HOH HOH D . J 3 HOH 10 310 7 HOH HOH D . J 3 HOH 11 311 10 HOH HOH D . J 3 HOH 12 312 52 HOH HOH D . J 3 HOH 13 313 62 HOH HOH D . J 3 HOH 14 314 64 HOH HOH D . J 3 HOH 15 315 65 HOH HOH D . J 3 HOH 16 316 41 HOH HOH D . J 3 HOH 17 317 50 HOH HOH D . J 3 HOH 18 318 43 HOH HOH D . J 3 HOH 19 319 57 HOH HOH D . # 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 ? ? ? 1.9_1692 1 ? 'data collection' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? v706e 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? v706e 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.15 5 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? v706e 6 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.9_1692 7 # _cell.length_a 44.059 _cell.length_b 44.059 _cell.length_c 85.398 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 5DEK _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.entry_id 5DEK _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # _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 5DEK _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 2.08 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 40.84 _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, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 5.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 20 mM MgCl2, 80 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 CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-11-02 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Si(111)' _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 0.97856 _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 21-ID-G' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97856 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-G _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 40.4550168222 _reflns.entry_id 5DEK _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.000 _reflns.d_resolution_low 39.15 _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 10680 _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 97.600 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 12.800 _reflns.pdbx_Rmerge_I_obs 0.126 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 15.113 _reflns.pdbx_netI_over_sigmaI 7.500 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.059 _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 0.128 _reflns.pdbx_Rpim_I_all 0.038 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 77578 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # 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_all _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 _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 _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 2.000 2.030 ? 1.8 ? ? ? ? ? 96.600 ? ? ? ? 0.682 ? ? ? ? ? ? ? ? 7.500 ? ? ? ? ? ? ? 1 1 ? ? 2.030 2.070 ? ? ? ? ? ? ? 97.300 ? ? ? ? 0.940 ? ? ? ? ? ? ? ? 8.700 ? ? ? ? ? ? ? 2 1 ? ? 2.070 2.110 ? ? ? ? ? ? ? 97.000 ? ? ? ? ? ? ? ? ? ? ? ? ? 9.700 ? ? ? ? ? ? ? 3 1 ? ? 2.110 2.150 ? ? ? ? ? ? ? 97.000 ? ? ? ? ? ? ? ? ? ? ? ? ? 11.600 ? ? ? ? ? ? ? 4 1 ? ? 2.150 2.200 ? ? ? ? ? ? ? 97.000 ? ? ? ? 0.997 ? ? ? ? ? ? ? ? 12.700 ? ? ? ? ? ? ? 5 1 ? ? 2.200 2.250 ? ? ? ? ? ? ? 97.100 ? ? ? ? 0.912 ? ? ? ? ? ? ? ? 13.700 ? ? ? ? ? ? ? 6 1 ? ? 2.250 2.310 ? ? ? ? ? ? ? 97.300 ? ? ? ? 0.745 ? ? ? ? ? ? ? ? 14.200 ? ? ? ? ? ? ? 7 1 ? ? 2.310 2.370 ? ? ? ? ? ? ? 97.300 ? ? ? ? 0.630 ? ? ? ? ? ? ? ? 14.200 ? ? ? ? ? ? ? 8 1 ? ? 2.370 2.440 ? ? ? ? ? ? ? 97.700 ? ? ? ? 0.572 ? ? ? ? ? ? ? ? 14.200 ? ? ? ? ? ? ? 9 1 ? ? 2.440 2.520 ? ? ? ? ? ? ? 98.000 ? ? ? ? 0.460 ? ? ? ? ? ? ? ? 14.100 ? ? ? ? ? ? ? 10 1 ? ? 2.520 2.610 ? ? ? ? ? ? ? 98.100 ? ? ? ? 0.356 ? ? ? ? ? ? ? ? 14.000 ? ? ? ? ? ? ? 11 1 ? ? 2.610 2.710 ? ? ? ? ? ? ? 98.300 ? ? ? ? 0.254 ? ? ? ? ? ? ? ? 14.300 ? ? ? ? ? ? ? 12 1 ? ? 2.710 2.840 ? ? ? ? ? ? ? 97.700 ? ? ? ? 0.254 ? ? ? ? ? ? ? ? 13.900 ? ? ? ? ? ? ? 13 1 ? ? 2.840 2.990 ? ? ? ? ? ? ? 97.800 ? ? ? ? 0.189 ? ? ? ? ? ? ? ? 14.100 ? ? ? ? ? ? ? 14 1 ? ? 2.990 3.170 ? ? ? ? ? ? ? 97.200 ? ? ? ? 0.164 ? ? ? ? ? ? ? ? 13.600 ? ? ? ? ? ? ? 15 1 ? ? 3.170 3.420 ? ? ? ? ? ? ? 97.100 ? ? ? ? 0.132 ? ? ? ? ? ? ? ? 13.700 ? ? ? ? ? ? ? 16 1 ? ? 3.420 3.760 ? ? ? ? ? ? ? 97.800 ? ? ? ? 0.117 ? ? ? ? ? ? ? ? 13.700 ? ? ? ? ? ? ? 17 1 ? ? 3.760 4.310 ? ? ? ? ? ? ? 98.400 ? ? ? ? 0.095 ? ? ? ? ? ? ? ? 13.300 ? ? ? ? ? ? ? 18 1 ? ? 4.310 5.430 ? ? ? ? ? ? ? 98.800 ? ? ? ? 0.081 ? ? ? ? ? ? ? ? 12.900 ? ? ? ? ? ? ? 19 1 ? ? 5.430 50.000 ? ? ? ? ? ? ? 97.400 ? ? ? ? 0.081 ? ? ? ? ? ? ? ? 11.300 ? ? ? ? ? ? ? 20 1 ? ? # _refine.entry_id 5DEK _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 1.9930 _refine.ls_d_res_low 39.1550 _refine.pdbx_ls_sigma_F 0.410 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 97.4500 _refine.ls_number_reflns_obs 10680 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2411 _refine.ls_R_factor_R_work 0.2400 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2621 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.2300 _refine.ls_number_reflns_R_free 559 _refine.ls_number_reflns_R_work 10121 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 41.8983 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.3500 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 100.870 _refine.B_iso_min 30.290 _refine.pdbx_overall_phase_error 34.9500 _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.9930 _refine_hist.d_res_low 39.1550 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 66 _refine_hist.number_atoms_total 748 _refine_hist.pdbx_number_residues_total 32 _refine_hist.pdbx_B_iso_mean_ligand 66.91 _refine_hist.pdbx_B_iso_mean_solvent 49.56 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 668 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' f_bond_d 756 0.001 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 1182 0.303 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 152 0.010 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 32 0.001 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 360 4.952 ? ? ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.R_factor_obs 1.9931 2.1937 4 97.0000 2500 . 0.3242 0.3980 . 145 . 2645 . 'X-RAY DIFFRACTION' . 2.1937 2.5111 4 98.0000 2546 . 0.3038 0.3437 . 142 . 2688 . 'X-RAY DIFFRACTION' . 2.5111 3.1635 4 98.0000 2557 . 0.2924 0.2562 . 134 . 2691 . 'X-RAY DIFFRACTION' . 3.1635 39.1625 4 97.0000 2518 . 0.1894 0.2275 . 138 . 2656 . 'X-RAY DIFFRACTION' . # _struct.entry_id 5DEK _struct.title 'RNA octamer containing dT' _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 5DEK _struct_keywords.text 'RNA, oligonucleotide' _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 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5DEK _struct_ref.pdbx_db_accession 5DEK _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 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 5DEK A 1 ? 8 ? 5DEK 101 ? 108 ? 101 108 2 1 5DEK B 1 ? 8 ? 5DEK 209 ? 216 ? 209 216 3 1 5DEK C 1 ? 8 ? 5DEK 101 ? 108 ? 101 108 4 1 5DEK D 1 ? 8 ? 5DEK 209 ? 216 ? 209 216 # 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_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 930 ? 1 MORE -5 ? 1 'SSA (A^2)' 3210 ? 2 'ABSA (A^2)' 940 ? 2 MORE -4 ? 2 'SSA (A^2)' 3210 ? # 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,G,H 2 1 C,D,F,I,J # _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_ _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 C 1 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 101 B G 216 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 101 B G 216 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 101 B G 216 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 102 B C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 102 B C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 102 B C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 103 B U 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 103 B U 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 4 N1 ? ? ? 1_555 B DT 5 N3 ? ? A A 104 B DT 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N6 ? ? ? 1_555 B DT 5 O4 ? ? A A 104 B DT 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B A 4 N1 ? ? A DT 105 B A 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B A 4 N6 ? ? A DT 105 B A 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 106 B A 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 106 B A 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 107 B G 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 107 B G 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 107 B G 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 108 B C 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 108 B C 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 108 B C 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C C 1 N3 ? ? ? 1_555 D G 8 N1 ? ? C C 101 D G 216 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C C 1 N4 ? ? ? 1_555 D G 8 O6 ? ? C C 101 D G 216 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C C 1 O2 ? ? ? 1_555 D G 8 N2 ? ? C C 101 D G 216 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 7 N3 ? ? C G 102 D C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C G 2 N2 ? ? ? 1_555 D C 7 O2 ? ? C G 102 D C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C G 2 O6 ? ? ? 1_555 D C 7 N4 ? ? C G 102 D C 215 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C A 3 N1 ? ? ? 1_555 D U 6 N3 ? ? C A 103 D U 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C A 3 N6 ? ? ? 1_555 D U 6 O4 ? ? C A 103 D U 214 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C A 4 N1 ? ? ? 1_555 D DT 5 N3 ? ? C A 104 D DT 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C A 4 N6 ? ? ? 1_555 D DT 5 O4 ? ? C A 104 D DT 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C DT 5 N3 ? ? ? 1_555 D A 4 N1 ? ? C DT 105 D A 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DT 5 O4 ? ? ? 1_555 D A 4 N6 ? ? C DT 105 D A 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C U 6 N3 ? ? ? 1_555 D A 3 N1 ? ? C U 106 D A 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C U 6 O4 ? ? ? 1_555 D A 3 N6 ? ? C U 106 D A 211 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C C 7 N3 ? ? ? 1_555 D G 2 N1 ? ? C C 107 D G 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C C 7 N4 ? ? ? 1_555 D G 2 O6 ? ? C C 107 D G 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C C 7 O2 ? ? ? 1_555 D G 2 N2 ? ? C C 107 D G 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C G 8 N1 ? ? ? 1_555 D C 1 N3 ? ? C G 108 D C 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C G 8 N2 ? ? ? 1_555 D C 1 O2 ? ? C G 108 D C 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C G 8 O6 ? ? ? 1_555 D C 1 N4 ? ? C G 108 D C 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B NCO 301 ? 6 'binding site for residue NCO B 301' AC2 Software C NCO 201 ? 6 'binding site for residue NCO C 201' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 C A 7 ? C A 107 . ? 4_455 ? 2 AC1 6 G A 8 ? G A 108 . ? 4_455 ? 3 AC1 6 A B 4 ? A B 212 . ? 1_555 ? 4 AC1 6 HOH H . ? HOH B 405 . ? 1_555 ? 5 AC1 6 U C 6 ? U C 106 . ? 6_455 ? 6 AC1 6 C C 7 ? C C 107 . ? 6_455 ? 7 AC2 6 U A 6 ? U A 106 . ? 7_555 ? 8 AC2 6 C A 7 ? C A 107 . ? 7_555 ? 9 AC2 6 A C 3 ? A C 103 . ? 7_555 ? 10 AC2 6 A C 4 ? A C 104 . ? 7_555 ? 11 AC2 6 G C 8 ? G C 108 . ? 1_555 ? 12 AC2 6 HOH I . ? HOH C 301 . ? 1_555 ? # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y+1/2,x+1/2,z+3/4 3 y+1/2,-x+1/2,z+1/4 4 x+1/2,-y+1/2,-z+1/4 5 -x+1/2,y+1/2,-z+3/4 6 -x,-y,z+1/2 7 y,x,-z 8 -y,-x,-z+1/2 # _diffrn_reflns.diffrn_id 1 _diffrn_reflns.pdbx_d_res_high 2.000 _diffrn_reflns.pdbx_d_res_low 50.000 _diffrn_reflns.pdbx_number_obs 6070 _diffrn_reflns.pdbx_Rmerge_I_obs 0.126 _diffrn_reflns.pdbx_Rsym_value ? _diffrn_reflns.pdbx_chi_squared 1.06 _diffrn_reflns.pdbx_redundancy 12.80 _diffrn_reflns.pdbx_rejects ? _diffrn_reflns.pdbx_percent_possible_obs 97.60 _diffrn_reflns.pdbx_observed_criterion ? _diffrn_reflns.number 77578 _diffrn_reflns.limit_h_max ? _diffrn_reflns.limit_h_min ? _diffrn_reflns.limit_k_max ? _diffrn_reflns.limit_k_min ? _diffrn_reflns.limit_l_max ? _diffrn_reflns.limit_l_min ? # loop_ _pdbx_diffrn_reflns_shell.diffrn_id _pdbx_diffrn_reflns_shell.d_res_high _pdbx_diffrn_reflns_shell.d_res_low _pdbx_diffrn_reflns_shell.number_obs _pdbx_diffrn_reflns_shell.rejects _pdbx_diffrn_reflns_shell.Rmerge_I_obs _pdbx_diffrn_reflns_shell.Rsym_value _pdbx_diffrn_reflns_shell.chi_squared _pdbx_diffrn_reflns_shell.redundancy _pdbx_diffrn_reflns_shell.percent_possible_obs 1 5.43 50.00 ? ? 0.081 ? 1.116 11.30 ? 1 4.31 5.43 ? ? 0.081 ? 1.068 12.90 ? 1 3.76 4.31 ? ? 0.095 ? 1.069 13.30 ? 1 3.42 3.76 ? ? 0.117 ? 1.070 13.70 ? 1 3.17 3.42 ? ? 0.132 ? 1.055 13.70 ? 1 2.99 3.17 ? ? 0.164 ? 1.175 13.60 ? 1 2.84 2.99 ? ? 0.189 ? 1.175 14.10 ? 1 2.71 2.84 ? ? 0.254 ? 1.173 13.90 ? 1 2.61 2.71 ? ? 0.254 ? 1.175 14.30 ? 1 2.52 2.61 ? ? 0.356 ? 1.071 14.00 ? 1 2.44 2.52 ? ? 0.460 ? 1.021 14.10 ? 1 2.37 2.44 ? ? 0.572 ? 0.981 14.20 ? 1 2.31 2.37 ? ? 0.630 ? 0.992 14.20 ? 1 2.25 2.31 ? ? 0.745 ? 0.978 14.20 ? 1 2.20 2.25 ? ? 0.912 ? 0.993 13.70 ? 1 2.15 2.20 ? ? 0.997 ? 0.997 12.70 ? 1 2.11 2.15 ? ? ? ? 0.948 11.60 ? 1 2.07 2.11 ? ? ? ? 0.991 9.70 ? 1 2.03 2.07 ? ? 0.940 ? 0.980 8.70 ? 1 2.00 2.03 ? ? 0.974 ? 1.062 7.50 ? # _phasing.method MR # 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 DT OP3 O N N 73 DT P P N N 74 DT OP1 O N N 75 DT OP2 O N N 76 DT "O5'" O N N 77 DT "C5'" C N N 78 DT "C4'" C N R 79 DT "O4'" O N N 80 DT "C3'" C N S 81 DT "O3'" O N N 82 DT "C2'" C N N 83 DT "C1'" C N R 84 DT N1 N N N 85 DT C2 C N N 86 DT O2 O N N 87 DT N3 N N N 88 DT C4 C N N 89 DT O4 O N N 90 DT C5 C N N 91 DT C7 C N N 92 DT C6 C N N 93 DT HOP3 H N N 94 DT HOP2 H N N 95 DT "H5'" H N N 96 DT "H5''" H N N 97 DT "H4'" H N N 98 DT "H3'" H N N 99 DT "HO3'" H N N 100 DT "H2'" H N N 101 DT "H2''" H N N 102 DT "H1'" H N N 103 DT H3 H N N 104 DT H71 H N N 105 DT H72 H N N 106 DT H73 H N N 107 DT H6 H N N 108 G OP3 O N N 109 G P P N N 110 G OP1 O N N 111 G OP2 O N N 112 G "O5'" O N N 113 G "C5'" C N N 114 G "C4'" C N R 115 G "O4'" O N N 116 G "C3'" C N S 117 G "O3'" O N N 118 G "C2'" C N R 119 G "O2'" O N N 120 G "C1'" C N R 121 G N9 N Y N 122 G C8 C Y N 123 G N7 N Y N 124 G C5 C Y N 125 G C6 C N N 126 G O6 O N N 127 G N1 N N N 128 G C2 C N N 129 G N2 N N N 130 G N3 N N N 131 G C4 C Y N 132 G HOP3 H N N 133 G HOP2 H N N 134 G "H5'" H N N 135 G "H5''" H N N 136 G "H4'" H N N 137 G "H3'" H N N 138 G "HO3'" H N N 139 G "H2'" H N N 140 G "HO2'" H N N 141 G "H1'" H N N 142 G H8 H N N 143 G H1 H N N 144 G H21 H N N 145 G H22 H N N 146 HOH O O N N 147 HOH H1 H N N 148 HOH H2 H N N 149 NCO CO CO N N 150 NCO N1 N N N 151 NCO N2 N N N 152 NCO N3 N N N 153 NCO N4 N N N 154 NCO N5 N N N 155 NCO N6 N N N 156 NCO HN11 H N N 157 NCO HN12 H N N 158 NCO HN13 H N N 159 NCO HN21 H N N 160 NCO HN22 H N N 161 NCO HN23 H N N 162 NCO HN31 H N N 163 NCO HN32 H N N 164 NCO HN33 H N N 165 NCO HN41 H N N 166 NCO HN42 H N N 167 NCO HN43 H N N 168 NCO HN51 H N N 169 NCO HN52 H N N 170 NCO HN53 H N N 171 NCO HN61 H N N 172 NCO HN62 H N N 173 NCO HN63 H N N 174 U OP3 O N N 175 U P P N N 176 U OP1 O N N 177 U OP2 O N N 178 U "O5'" O N N 179 U "C5'" C N N 180 U "C4'" C N R 181 U "O4'" O N N 182 U "C3'" C N S 183 U "O3'" O N N 184 U "C2'" C N R 185 U "O2'" O N N 186 U "C1'" C N R 187 U N1 N N N 188 U C2 C N N 189 U O2 O N N 190 U N3 N N N 191 U C4 C N N 192 U O4 O N N 193 U C5 C N N 194 U C6 C N N 195 U HOP3 H N N 196 U HOP2 H N N 197 U "H5'" H N N 198 U "H5''" H N N 199 U "H4'" H N N 200 U "H3'" H N N 201 U "HO3'" H N N 202 U "H2'" H N N 203 U "HO2'" H N N 204 U "H1'" H N N 205 U H3 H N N 206 U H5 H N N 207 U H6 H N N 208 # 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 DT OP3 P sing N N 76 DT OP3 HOP3 sing N N 77 DT P OP1 doub N N 78 DT P OP2 sing N N 79 DT P "O5'" sing N N 80 DT OP2 HOP2 sing N N 81 DT "O5'" "C5'" sing N N 82 DT "C5'" "C4'" sing N N 83 DT "C5'" "H5'" sing N N 84 DT "C5'" "H5''" sing N N 85 DT "C4'" "O4'" sing N N 86 DT "C4'" "C3'" sing N N 87 DT "C4'" "H4'" sing N N 88 DT "O4'" "C1'" sing N N 89 DT "C3'" "O3'" sing N N 90 DT "C3'" "C2'" sing N N 91 DT "C3'" "H3'" sing N N 92 DT "O3'" "HO3'" sing N N 93 DT "C2'" "C1'" sing N N 94 DT "C2'" "H2'" sing N N 95 DT "C2'" "H2''" sing N N 96 DT "C1'" N1 sing N N 97 DT "C1'" "H1'" sing N N 98 DT N1 C2 sing N N 99 DT N1 C6 sing N N 100 DT C2 O2 doub N N 101 DT C2 N3 sing N N 102 DT N3 C4 sing N N 103 DT N3 H3 sing N N 104 DT C4 O4 doub N N 105 DT C4 C5 sing N N 106 DT C5 C7 sing N N 107 DT C5 C6 doub N N 108 DT C7 H71 sing N N 109 DT C7 H72 sing N N 110 DT C7 H73 sing N N 111 DT C6 H6 sing N N 112 G OP3 P sing N N 113 G OP3 HOP3 sing N N 114 G P OP1 doub N N 115 G P OP2 sing N N 116 G P "O5'" sing N N 117 G OP2 HOP2 sing N N 118 G "O5'" "C5'" sing N N 119 G "C5'" "C4'" sing N N 120 G "C5'" "H5'" sing N N 121 G "C5'" "H5''" sing N N 122 G "C4'" "O4'" sing N N 123 G "C4'" "C3'" sing N N 124 G "C4'" "H4'" sing N N 125 G "O4'" "C1'" sing N N 126 G "C3'" "O3'" sing N N 127 G "C3'" "C2'" sing N N 128 G "C3'" "H3'" sing N N 129 G "O3'" "HO3'" sing N N 130 G "C2'" "O2'" sing N N 131 G "C2'" "C1'" sing N N 132 G "C2'" "H2'" sing N N 133 G "O2'" "HO2'" sing N N 134 G "C1'" N9 sing N N 135 G "C1'" "H1'" sing N N 136 G N9 C8 sing Y N 137 G N9 C4 sing Y N 138 G C8 N7 doub Y N 139 G C8 H8 sing N N 140 G N7 C5 sing Y N 141 G C5 C6 sing N N 142 G C5 C4 doub Y N 143 G C6 O6 doub N N 144 G C6 N1 sing N N 145 G N1 C2 sing N N 146 G N1 H1 sing N N 147 G C2 N2 sing N N 148 G C2 N3 doub N N 149 G N2 H21 sing N N 150 G N2 H22 sing N N 151 G N3 C4 sing N N 152 HOH O H1 sing N N 153 HOH O H2 sing N N 154 NCO CO N1 sing N N 155 NCO CO N2 sing N N 156 NCO CO N3 sing N N 157 NCO CO N4 sing N N 158 NCO CO N5 sing N N 159 NCO CO N6 sing N N 160 NCO N1 HN11 sing N N 161 NCO N1 HN12 sing N N 162 NCO N1 HN13 sing N N 163 NCO N2 HN21 sing N N 164 NCO N2 HN22 sing N N 165 NCO N2 HN23 sing N N 166 NCO N3 HN31 sing N N 167 NCO N3 HN32 sing N N 168 NCO N3 HN33 sing N N 169 NCO N4 HN41 sing N N 170 NCO N4 HN42 sing N N 171 NCO N4 HN43 sing N N 172 NCO N5 HN51 sing N N 173 NCO N5 HN52 sing N N 174 NCO N5 HN53 sing N N 175 NCO N6 HN61 sing N N 176 NCO N6 HN62 sing N N 177 NCO N6 HN63 sing N N 178 U OP3 P sing N N 179 U OP3 HOP3 sing N N 180 U P OP1 doub N N 181 U P OP2 sing N N 182 U P "O5'" sing N N 183 U OP2 HOP2 sing N N 184 U "O5'" "C5'" sing N N 185 U "C5'" "C4'" sing N N 186 U "C5'" "H5'" sing N N 187 U "C5'" "H5''" sing N N 188 U "C4'" "O4'" sing N N 189 U "C4'" "C3'" sing N N 190 U "C4'" "H4'" sing N N 191 U "O4'" "C1'" sing N N 192 U "C3'" "O3'" sing N N 193 U "C3'" "C2'" sing N N 194 U "C3'" "H3'" sing N N 195 U "O3'" "HO3'" sing N N 196 U "C2'" "O2'" sing N N 197 U "C2'" "C1'" sing N N 198 U "C2'" "H2'" sing N N 199 U "O2'" "HO2'" sing N N 200 U "C1'" N1 sing N N 201 U "C1'" "H1'" sing N N 202 U N1 C2 sing N N 203 U N1 C6 sing N N 204 U C2 O2 doub N N 205 U C2 N3 sing N N 206 U N3 C4 sing N N 207 U N3 H3 sing N N 208 U C4 O4 doub N N 209 U C4 C5 sing N N 210 U C5 C6 doub N N 211 U C5 H5 sing N N 212 U C6 H6 sing N N 213 # _ndb_struct_conf_na.entry_id 5DEK _ndb_struct_conf_na.feature '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 C 1 1_555 B G 8 1_555 0.110 -0.081 -0.221 10.185 -17.630 2.134 1 A_C101:G216_B A 101 ? B 216 ? 19 1 1 A G 2 1_555 B C 7 1_555 -0.446 -0.191 -0.101 -6.030 -10.219 1.776 2 A_G102:C215_B A 102 ? B 215 ? 19 1 1 A A 3 1_555 B U 6 1_555 0.187 -0.181 -0.318 -7.853 -13.205 -0.798 3 A_A103:U214_B A 103 ? B 214 ? 20 1 1 A A 4 1_555 B DT 5 1_555 -0.228 -0.203 0.084 -3.197 -12.824 2.675 4 A_A104:DT213_B A 104 ? B 213 ? 20 1 1 A DT 5 1_555 B A 4 1_555 0.321 -0.212 0.022 6.111 -12.984 -1.749 5 A_DT105:A212_B A 105 ? B 212 ? 20 1 1 A U 6 1_555 B A 3 1_555 -0.056 -0.203 -0.339 9.008 -9.981 -1.975 6 A_U106:A211_B A 106 ? B 211 ? 20 1 1 A C 7 1_555 B G 2 1_555 0.272 -0.203 -0.075 3.876 -14.386 2.729 7 A_C107:G210_B A 107 ? B 210 ? 19 1 1 A G 8 1_555 B C 1 1_555 -0.111 -0.110 -0.310 -13.640 -19.718 -1.629 8 A_G108:C209_B A 108 ? B 209 ? 19 1 1 C C 1 1_555 D G 8 1_555 0.185 -0.050 -0.241 13.876 -18.211 -0.936 9 C_C101:G216_D C 101 ? D 216 ? 19 1 1 C G 2 1_555 D C 7 1_555 -0.487 -0.249 -0.085 -5.206 -14.588 2.497 10 C_G102:C215_D C 102 ? D 215 ? 19 1 1 C A 3 1_555 D U 6 1_555 -0.012 -0.199 -0.301 -10.128 -11.761 -1.464 11 C_A103:U214_D C 103 ? D 214 ? 20 1 1 C A 4 1_555 D DT 5 1_555 -0.071 -0.170 -0.064 -6.796 -11.681 0.427 12 C_A104:DT213_D C 104 ? D 213 ? 20 1 1 C DT 5 1_555 D A 4 1_555 0.405 -0.235 -0.015 3.263 -8.737 -0.201 13 C_DT105:A212_D C 105 ? D 212 ? 20 1 1 C U 6 1_555 D A 3 1_555 -0.011 -0.167 -0.355 7.912 -8.894 -0.352 14 C_U106:A211_D C 106 ? D 211 ? 20 1 1 C C 7 1_555 D G 2 1_555 0.004 -0.169 -0.287 5.470 -14.825 2.618 15 C_C107:G210_D C 107 ? D 210 ? 19 1 1 C G 8 1_555 D C 1 1_555 -0.688 -0.273 -0.316 -10.090 -18.792 3.086 16 C_G108:C209_D C 108 ? D 209 ? 19 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 C 1 1_555 B G 8 1_555 A G 2 1_555 B C 7 1_555 -0.270 -1.672 3.565 -4.064 13.244 31.446 -4.914 -0.179 2.678 23.085 7.084 34.291 1 AA_C101G102:C215G216_BB A 101 ? B 216 ? A 102 ? B 215 ? 1 A G 2 1_555 B C 7 1_555 A A 3 1_555 B U 6 1_555 -0.336 -1.335 3.273 1.285 9.413 35.330 -3.361 0.704 2.823 15.174 -2.071 36.546 2 AA_G102A103:U214C215_BB A 102 ? B 215 ? A 103 ? B 214 ? 1 A A 3 1_555 B U 6 1_555 A A 4 1_555 B DT 5 1_555 0.072 -1.085 3.023 -1.873 10.535 30.577 -3.570 -0.417 2.512 19.252 3.422 32.353 3 AA_A103A104:DT213U214_BB A 103 ? B 214 ? A 104 ? B 213 ? 1 A A 4 1_555 B DT 5 1_555 A DT 5 1_555 B A 4 1_555 -0.242 -1.200 2.998 -0.050 9.392 33.870 -3.211 0.394 2.584 15.749 0.084 35.112 4 AA_A104DT105:A212DT213_BB A 104 ? B 213 ? A 105 ? B 212 ? 1 A DT 5 1_555 B A 4 1_555 A U 6 1_555 B A 3 1_555 0.286 -1.275 3.171 2.328 5.068 30.319 -3.330 -0.110 2.937 9.588 -4.403 30.815 5 AA_DT105U106:A211A212_BB A 105 ? B 212 ? A 106 ? B 211 ? 1 A U 6 1_555 B A 3 1_555 A C 7 1_555 B G 2 1_555 0.522 -1.494 3.208 0.511 11.430 34.791 -3.820 -0.767 2.612 18.507 -0.827 36.569 6 AA_U106C107:G210A211_BB A 106 ? B 211 ? A 107 ? B 210 ? 1 A C 7 1_555 B G 2 1_555 A G 8 1_555 B C 1 1_555 0.071 -1.657 3.559 4.162 15.286 33.810 -4.602 0.436 2.589 24.673 -6.718 37.239 7 AA_C107G108:C209G210_BB A 107 ? B 210 ? A 108 ? B 209 ? 1 C C 1 1_555 D G 8 1_555 C G 2 1_555 D C 7 1_555 -0.183 -1.607 3.540 -4.366 15.411 33.239 -4.614 -0.297 2.575 25.202 7.140 36.799 8 CC_C101G102:C215G216_DD C 101 ? D 216 ? C 102 ? D 215 ? 1 C G 2 1_555 D C 7 1_555 C A 3 1_555 D U 6 1_555 -0.433 -1.281 3.300 -0.931 9.755 35.567 -3.297 0.563 2.871 15.606 1.489 36.850 9 CC_G102A103:U214C215_DD C 102 ? D 215 ? C 103 ? D 214 ? 1 C A 3 1_555 D U 6 1_555 C A 4 1_555 D DT 5 1_555 -0.142 -1.233 3.163 -1.187 6.422 31.599 -3.284 0.058 2.867 11.638 2.151 32.250 10 CC_A103A104:DT213U214_DD C 103 ? D 214 ? C 104 ? D 213 ? 1 C A 4 1_555 D DT 5 1_555 C DT 5 1_555 D A 4 1_555 -0.029 -1.166 3.046 -0.277 9.922 32.777 -3.362 0.010 2.593 17.099 0.478 34.208 11 CC_A104DT105:A212DT213_DD C 104 ? D 213 ? C 105 ? D 212 ? 1 C DT 5 1_555 D A 4 1_555 C U 6 1_555 D A 3 1_555 0.091 -1.341 3.119 1.013 8.021 29.116 -4.044 0.011 2.665 15.579 -1.968 30.194 12 CC_DT105U106:A211A212_DD C 105 ? D 212 ? C 106 ? D 211 ? 1 C U 6 1_555 D A 3 1_555 C C 7 1_555 D G 2 1_555 0.326 -1.443 3.270 1.413 10.851 32.403 -4.062 -0.346 2.674 18.788 -2.446 34.154 13 CC_U106C107:G210A211_DD C 106 ? D 211 ? C 107 ? D 210 ? 1 C C 7 1_555 D G 2 1_555 C G 8 1_555 D C 1 1_555 0.472 -1.752 3.555 2.114 16.330 29.627 -5.554 -0.482 2.328 29.263 -3.788 33.805 14 CC_C107G108:C209G210_DD C 107 ? D 210 ? C 108 ? D 209 ? # _space_group.name_H-M_alt 'P 43 21 2' _space_group.name_Hall 'P 4nw 2abw' _space_group.IT_number 96 _space_group.crystal_system tetragonal _space_group.id 1 # _atom_sites.entry_id 5DEK _atom_sites.fract_transf_matrix[1][1] 0.022697 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.022697 _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] 0.011710 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # 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_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 25.62398 1.50364 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? CO ? ? ? ? ? ? ? ? ? N ? ? 4.01032 2.96436 19.97189 1.75589 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 15.80542 1.70748 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 1.42069 35.72801 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_