data_7ULY # _entry.id 7ULY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.366 _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 7ULY pdb_00007uly 10.2210/pdb7uly/pdb WWPDB D_1000264237 ? ? EMDB EMD-26596 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'MicroED structure of triclinic lysozyme' _pdbx_database_related.db_id EMD-26596 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7ULY _pdbx_database_status.recvd_initial_deposition_date 2022-04-05 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Clabbers, M.T.B.' 1 0000-0002-5466-6508 'Martynowycz, M.W.' 2 0000-0003-0055-230X 'Hattne, J.' 3 0000-0002-8936-0912 'Gonen, T.' 4 0000-0002-9254-4069 # _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 NE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'J Struct Biol X' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2590-1524 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 6 _citation.language ? _citation.page_first 100078 _citation.page_last 100078 _citation.title 'Hydrogens and hydrogen-bond networks in macromolecular MicroED data.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.yjsbx.2022.100078 _citation.pdbx_database_id_PubMed 36507068 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Clabbers, M.T.B.' 1 ? primary 'Martynowycz, M.W.' 2 ? primary 'Hattne, J.' 3 ? primary 'Gonen, T.' 4 ? # _cell.angle_alpha 88.319 _cell.angle_alpha_esd ? _cell.angle_beta 109.095 _cell.angle_beta_esd ? _cell.angle_gamma 112.075 _cell.angle_gamma_esd ? _cell.entry_id 7ULY _cell.details ? _cell.formula_units_Z ? _cell.length_a 26.420 _cell.length_a_esd ? _cell.length_b 30.720 _cell.length_b_esd ? _cell.length_c 33.010 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 1 _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 7ULY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _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 nat 'Lysozyme C' 14331.160 1 3.2.1.17 ? ? ? 2 non-polymer syn 'NITRATE ION' 62.005 4 ? ? ? ? 3 water nat water 18.015 112 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name '1,4-beta-N-acetylmuramidase C,Allergen Gal d IV' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPC SALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL ; _entity_poly.pdbx_seq_one_letter_code_can ;KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPC SALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LYS n 1 2 VAL n 1 3 PHE n 1 4 GLY n 1 5 ARG n 1 6 CYS n 1 7 GLU n 1 8 LEU n 1 9 ALA n 1 10 ALA n 1 11 ALA n 1 12 MET n 1 13 LYS n 1 14 ARG n 1 15 HIS n 1 16 GLY n 1 17 LEU n 1 18 ASP n 1 19 ASN n 1 20 TYR n 1 21 ARG n 1 22 GLY n 1 23 TYR n 1 24 SER n 1 25 LEU n 1 26 GLY n 1 27 ASN n 1 28 TRP n 1 29 VAL n 1 30 CYS n 1 31 ALA n 1 32 ALA n 1 33 LYS n 1 34 PHE n 1 35 GLU n 1 36 SER n 1 37 ASN n 1 38 PHE n 1 39 ASN n 1 40 THR n 1 41 GLN n 1 42 ALA n 1 43 THR n 1 44 ASN n 1 45 ARG n 1 46 ASN n 1 47 THR n 1 48 ASP n 1 49 GLY n 1 50 SER n 1 51 THR n 1 52 ASP n 1 53 TYR n 1 54 GLY n 1 55 ILE n 1 56 LEU n 1 57 GLN n 1 58 ILE n 1 59 ASN n 1 60 SER n 1 61 ARG n 1 62 TRP n 1 63 TRP n 1 64 CYS n 1 65 ASN n 1 66 ASP n 1 67 GLY n 1 68 ARG n 1 69 THR n 1 70 PRO n 1 71 GLY n 1 72 SER n 1 73 ARG n 1 74 ASN n 1 75 LEU n 1 76 CYS n 1 77 ASN n 1 78 ILE n 1 79 PRO n 1 80 CYS n 1 81 SER n 1 82 ALA n 1 83 LEU n 1 84 LEU n 1 85 SER n 1 86 SER n 1 87 ASP n 1 88 ILE n 1 89 THR n 1 90 ALA n 1 91 SER n 1 92 VAL n 1 93 ASN n 1 94 CYS n 1 95 ALA n 1 96 LYS n 1 97 LYS n 1 98 ILE n 1 99 VAL n 1 100 SER n 1 101 ASP n 1 102 GLY n 1 103 ASN n 1 104 GLY n 1 105 MET n 1 106 ASN n 1 107 ALA n 1 108 TRP n 1 109 VAL n 1 110 ALA n 1 111 TRP n 1 112 ARG n 1 113 ASN n 1 114 ARG n 1 115 CYS n 1 116 LYS n 1 117 GLY n 1 118 THR n 1 119 ASP n 1 120 VAL n 1 121 GLN n 1 122 ALA n 1 123 TRP n 1 124 ILE n 1 125 ARG n 1 126 GLY n 1 127 CYS n 1 128 ARG n 1 129 LEU n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num 1 _entity_src_nat.pdbx_end_seq_num 129 _entity_src_nat.common_name chicken _entity_src_nat.pdbx_organism_scientific 'Gallus gallus' _entity_src_nat.pdbx_ncbi_taxonomy_id 9031 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code LYSC_CHICK _struct_ref.pdbx_db_accession P00698 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPC SALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL ; _struct_ref.pdbx_align_begin 19 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7ULY _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 129 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P00698 _struct_ref_seq.db_align_beg 19 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 147 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 129 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NO3 non-polymer . 'NITRATE ION' ? 'N O3 -1' 62.005 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _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 7ULY _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON CRYSTALLOGRAPHY' _exptl.method_details ? # _refine.aniso_B[1][1] -1.180 _refine.aniso_B[1][2] -0.119 _refine.aniso_B[1][3] -0.194 _refine.aniso_B[2][2] 0.174 _refine.aniso_B[2][3] 0.142 _refine.aniso_B[3][3] 0.861 _refine.B_iso_max ? _refine.B_iso_mean 11.981 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.951 _refine.correlation_coeff_Fo_to_Fc_free 0.949 _refine.details 'Hydrogens have been added in their riding positions' _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 7ULY _refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _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 0.870 _refine.ls_d_res_low 19.876 _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 64974 _refine.ls_number_reflns_R_free 3168 _refine.ls_number_reflns_R_work 61806 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 87.578 _refine.ls_percent_reflns_R_free 4.876 _refine.ls_R_factor_all 0.198 _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free 0.2197 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1973 _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 'MASK BULK SOLVENT' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _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 THROUGHOUT _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.028 _refine.pdbx_overall_ESU_R_Free 0.028 _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _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 ? _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 1.286 _refine.overall_SU_ML 0.031 _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 ? # 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 'ELECTRON CRYSTALLOGRAPHY' ? 0.034 0.013 1138 ? r_bond_refined_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.000 0.014 1042 ? r_bond_other_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 2.447 1.637 1550 ? r_angle_refined_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 2.076 1.600 2390 ? r_angle_other_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 7.093 5.000 148 ? r_dihedral_angle_1_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 32.080 20.294 68 ? r_dihedral_angle_2_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 14.231 15.000 188 ? r_dihedral_angle_3_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 17.175 15.000 13 ? r_dihedral_angle_4_deg ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.169 0.200 141 ? r_chiral_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.012 0.020 1378 ? r_gen_planes_refined ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.005 0.020 316 ? r_gen_planes_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.248 0.200 404 ? r_nbd_refined ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.229 0.200 1515 ? r_symmetry_nbd_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.229 0.200 694 ? r_nbtor_refined ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.108 0.200 877 ? r_symmetry_nbtor_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.133 0.200 137 ? r_xyhbond_nbd_refined ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.278 0.200 28 ? r_symmetry_nbd_refined ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.198 0.200 90 ? r_nbd_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.129 0.200 39 ? r_symmetry_xyhbond_nbd_refined ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.342 1.017 558 ? r_mcbond_it ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.334 6.514 557 ? r_mcbond_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.577 1.522 708 ? r_mcangle_it ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.576 4.974 709 ? r_mcangle_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 5.338 1.292 580 ? r_scbond_it ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 5.291 4104.889 568 ? r_scbond_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 3.610 1.852 838 ? r_scangle_it ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 3.568 1.835 826 ? r_scangle_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 3.428 21.982 6885 ? r_lrange_it ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 3.320 21.743 6776 ? r_lrange_other ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 12.025 3.000 1138 ? r_rigid_bond_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_R_complete _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 'ELECTRON CRYSTALLOGRAPHY' 0.870 0.893 5493 . 94 1854 35.4633 . 0.388 . 0.385 . 0.388 . . . . . 0.390 . 20 . 0.016 0.012 'ELECTRON CRYSTALLOGRAPHY' 0.893 0.917 5367 . 166 3145 61.6918 . 0.461 . 0.476 . 0.460 . . . . . 0.476 . 20 . 0.033 0.024 'ELECTRON CRYSTALLOGRAPHY' 0.917 0.943 5201 . 185 3730 75.2740 . 0.430 . 0.451 . 0.429 . . . . . 0.436 . 20 . 0.629 0.668 'ELECTRON CRYSTALLOGRAPHY' 0.943 0.972 5004 . 193 3850 80.7954 . 0.376 . 0.393 . 0.375 . . . . . 0.370 . 20 . 0.799 0.767 'ELECTRON CRYSTALLOGRAPHY' 0.972 1.004 4894 . 246 4120 89.2113 . 0.343 . 0.362 . 0.341 . . . . . 0.326 . 20 . 0.866 0.861 'ELECTRON CRYSTALLOGRAPHY' 1.004 1.039 4714 . 208 4118 91.7692 . 0.287 . 0.314 . 0.286 . . . . . 0.266 . 20 . 0.911 0.923 'ELECTRON CRYSTALLOGRAPHY' 1.039 1.079 4553 . 212 4171 96.2662 . 0.221 . 0.244 . 0.220 . . . . . 0.199 . 20 . 0.944 0.941 'ELECTRON CRYSTALLOGRAPHY' 1.079 1.122 4397 . 227 4084 98.0441 . 0.178 . 0.209 . 0.176 . . . . . 0.156 . 20 . 0.957 0.945 'ELECTRON CRYSTALLOGRAPHY' 1.122 1.172 4213 . 189 3940 98.0062 . 0.158 . 0.199 . 0.156 . . . . . 0.134 . 20 . 0.962 0.953 'ELECTRON CRYSTALLOGRAPHY' 1.172 1.229 4046 . 174 3862 99.7528 . 0.156 . 0.196 . 0.154 . . . . . 0.132 . 20 . 0.959 0.954 'ELECTRON CRYSTALLOGRAPHY' 1.229 1.295 3816 . 192 3624 100.0000 . 0.147 . 0.180 . 0.146 . . . . . 0.125 . 20 . 0.961 0.956 'ELECTRON CRYSTALLOGRAPHY' 1.295 1.374 3624 . 178 3446 100.0000 . 0.158 . 0.185 . 0.156 . . . . . 0.142 . 20 . 0.959 0.951 'ELECTRON CRYSTALLOGRAPHY' 1.374 1.468 3446 . 176 3268 99.9420 . 0.162 . 0.183 . 0.160 . . . . . 0.152 . 20 . 0.962 0.953 'ELECTRON CRYSTALLOGRAPHY' 1.468 1.585 3140 . 142 2996 99.9363 . 0.182 . 0.206 . 0.181 . . . . . 0.172 . 20 . 0.942 0.925 'ELECTRON CRYSTALLOGRAPHY' 1.585 1.735 2934 . 150 2777 99.7614 . 0.176 . 0.206 . 0.175 . . . . . 0.166 . 20 . 0.950 0.949 'ELECTRON CRYSTALLOGRAPHY' 1.735 1.938 2645 . 110 2522 99.5085 . 0.178 . 0.200 . 0.177 . . . . . 0.169 . 20 . 0.935 0.920 'ELECTRON CRYSTALLOGRAPHY' 1.938 2.234 2324 . 100 2204 99.1394 . 0.176 . 0.207 . 0.175 . . . . . 0.161 . 20 . 0.927 0.891 'ELECTRON CRYSTALLOGRAPHY' 2.234 2.728 1973 . 94 1859 98.9863 . 0.173 . 0.220 . 0.171 . . . . . 0.170 . 20 . 0.936 0.919 'ELECTRON CRYSTALLOGRAPHY' 2.728 3.822 1535 . 89 1431 99.0228 . 0.213 . 0.199 . 0.213 . . . . . 0.208 . 20 . 0.929 0.935 'ELECTRON CRYSTALLOGRAPHY' 3.822 19.876 864 . 43 805 98.1481 . 0.312 . 0.293 . 0.313 . . . . . 0.307 . 20 . 0.913 0.922 # _struct.entry_id 7ULY _struct.title 'MicroED structure of triclinic lysozyme' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7ULY _struct_keywords.text Hydrolase _struct_keywords.pdbx_keywords HYDROLASE # 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 2 ? D N N 2 ? E N N 2 ? F N N 3 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 GLY A 4 ? HIS A 15 ? GLY A 4 HIS A 15 1 ? 12 HELX_P HELX_P2 AA2 ASN A 19 ? TYR A 23 ? ASN A 19 TYR A 23 5 ? 5 HELX_P HELX_P3 AA3 SER A 24 ? ASN A 37 ? SER A 24 ASN A 37 1 ? 14 HELX_P HELX_P4 AA4 PRO A 79 ? SER A 85 ? PRO A 79 SER A 85 5 ? 7 HELX_P HELX_P5 AA5 ILE A 88 ? ASP A 101 ? ILE A 88 ASP A 101 1 ? 14 HELX_P HELX_P6 AA6 GLY A 104 ? ALA A 107 ? GLY A 104 ALA A 107 5 ? 4 HELX_P HELX_P7 AA7 TRP A 108 ? CYS A 115 ? TRP A 108 CYS A 115 1 ? 8 HELX_P HELX_P8 AA8 ASP A 119 ? ILE A 124 ? ASP A 119 ILE A 124 5 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 disulf1 disulf ? ? A CYS 6 SG ? ? ? 1_555 A CYS 127 SG ? ? A CYS 6 A CYS 127 1_555 ? ? ? ? ? ? ? 1.964 ? ? disulf2 disulf ? ? A CYS 30 SG ? ? ? 1_555 A CYS 115 SG ? ? A CYS 30 A CYS 115 1_555 ? ? ? ? ? ? ? 1.999 ? ? disulf3 disulf ? ? A CYS 64 SG ? ? ? 1_555 A CYS 80 SG ? ? A CYS 64 A CYS 80 1_555 ? ? ? ? ? ? ? 1.968 ? ? disulf4 disulf ? ? A CYS 76 SG ? ? ? 1_555 A CYS 94 SG ? ? A CYS 76 A CYS 94 1_555 ? ? ? ? ? ? ? 1.986 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 3 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 THR A 43 ? ARG A 45 ? THR A 43 ARG A 45 AA1 2 THR A 51 ? TYR A 53 ? THR A 51 TYR A 53 AA1 3 ILE A 58 ? ASN A 59 ? ILE A 58 ASN A 59 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N ASN A 44 ? N ASN A 44 O ASP A 52 ? O ASP A 52 AA1 2 3 N TYR A 53 ? N TYR A 53 O ILE A 58 ? O ILE A 58 # _atom_sites.entry_id 7ULY _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.037850 _atom_sites.fract_transf_matrix[1][2] 0.015350 _atom_sites.fract_transf_matrix[1][3] 0.014829 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.035127 _atom_sites.fract_transf_matrix[2][3] 0.003777 _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] 0.032242 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c C 2.310 20.844 1.020 10.208 1.589 0.569 0.865 51.651 0.216 H 0.493 10.511 0.323 26.126 0.140 3.142 0.041 57.800 0.003 N 12.222 0.006 3.135 9.893 2.014 28.997 1.167 0.583 -11.538 O 3.049 13.277 2.287 5.701 1.546 0.324 0.867 32.909 0.251 S 6.905 1.468 5.203 22.215 1.438 0.254 1.586 56.172 0.867 # 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 LYS 1 1 1 LYS LYS A . n A 1 2 VAL 2 2 2 VAL VAL A . n A 1 3 PHE 3 3 3 PHE PHE A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 ARG 5 5 5 ARG ARG A . n A 1 6 CYS 6 6 6 CYS CYS A . n A 1 7 GLU 7 7 7 GLU GLU A . n A 1 8 LEU 8 8 8 LEU LEU A . n A 1 9 ALA 9 9 9 ALA ALA A . n A 1 10 ALA 10 10 10 ALA ALA A . n A 1 11 ALA 11 11 11 ALA ALA A . n A 1 12 MET 12 12 12 MET MET A . n A 1 13 LYS 13 13 13 LYS LYS A . n A 1 14 ARG 14 14 14 ARG ARG A . n A 1 15 HIS 15 15 15 HIS HIS A . n A 1 16 GLY 16 16 16 GLY GLY A . n A 1 17 LEU 17 17 17 LEU LEU A . n A 1 18 ASP 18 18 18 ASP ASP A . n A 1 19 ASN 19 19 19 ASN ASN A . n A 1 20 TYR 20 20 20 TYR TYR A . n A 1 21 ARG 21 21 21 ARG ARG A . n A 1 22 GLY 22 22 22 GLY GLY A . n A 1 23 TYR 23 23 23 TYR TYR A . n A 1 24 SER 24 24 24 SER SER A . n A 1 25 LEU 25 25 25 LEU LEU A . n A 1 26 GLY 26 26 26 GLY GLY A . n A 1 27 ASN 27 27 27 ASN ASN A . n A 1 28 TRP 28 28 28 TRP TRP A . n A 1 29 VAL 29 29 29 VAL VAL A . n A 1 30 CYS 30 30 30 CYS CYS A . n A 1 31 ALA 31 31 31 ALA ALA A . n A 1 32 ALA 32 32 32 ALA ALA A . n A 1 33 LYS 33 33 33 LYS LYS A . n A 1 34 PHE 34 34 34 PHE PHE A . n A 1 35 GLU 35 35 35 GLU GLU A . n A 1 36 SER 36 36 36 SER SER A . n A 1 37 ASN 37 37 37 ASN ASN A . n A 1 38 PHE 38 38 38 PHE PHE A . n A 1 39 ASN 39 39 39 ASN ASN A . n A 1 40 THR 40 40 40 THR THR A . n A 1 41 GLN 41 41 41 GLN GLN A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 THR 43 43 43 THR THR A . n A 1 44 ASN 44 44 44 ASN ASN A . n A 1 45 ARG 45 45 45 ARG ARG A . n A 1 46 ASN 46 46 46 ASN ASN A . n A 1 47 THR 47 47 47 THR THR A . n A 1 48 ASP 48 48 48 ASP ASP A . n A 1 49 GLY 49 49 49 GLY GLY A . n A 1 50 SER 50 50 50 SER SER A . n A 1 51 THR 51 51 51 THR THR A . n A 1 52 ASP 52 52 52 ASP ASP A . n A 1 53 TYR 53 53 53 TYR TYR A . n A 1 54 GLY 54 54 54 GLY GLY A . n A 1 55 ILE 55 55 55 ILE ILE A . n A 1 56 LEU 56 56 56 LEU LEU A . n A 1 57 GLN 57 57 57 GLN GLN A . n A 1 58 ILE 58 58 58 ILE ILE A . n A 1 59 ASN 59 59 59 ASN ASN A . n A 1 60 SER 60 60 60 SER SER A . n A 1 61 ARG 61 61 61 ARG ARG A . n A 1 62 TRP 62 62 62 TRP TRP A . n A 1 63 TRP 63 63 63 TRP TRP A . n A 1 64 CYS 64 64 64 CYS CYS A . n A 1 65 ASN 65 65 65 ASN ASN A . n A 1 66 ASP 66 66 66 ASP ASP A . n A 1 67 GLY 67 67 67 GLY GLY A . n A 1 68 ARG 68 68 68 ARG ARG A . n A 1 69 THR 69 69 69 THR THR A . n A 1 70 PRO 70 70 70 PRO PRO A . n A 1 71 GLY 71 71 71 GLY GLY A . n A 1 72 SER 72 72 72 SER SER A . n A 1 73 ARG 73 73 73 ARG ARG A . n A 1 74 ASN 74 74 74 ASN ASN A . n A 1 75 LEU 75 75 75 LEU LEU A . n A 1 76 CYS 76 76 76 CYS CYS A . n A 1 77 ASN 77 77 77 ASN ASN A . n A 1 78 ILE 78 78 78 ILE ILE A . n A 1 79 PRO 79 79 79 PRO PRO A . n A 1 80 CYS 80 80 80 CYS CYS A . n A 1 81 SER 81 81 81 SER SER A . n A 1 82 ALA 82 82 82 ALA ALA A . n A 1 83 LEU 83 83 83 LEU LEU A . n A 1 84 LEU 84 84 84 LEU LEU A . n A 1 85 SER 85 85 85 SER SER A . n A 1 86 SER 86 86 86 SER SER A . n A 1 87 ASP 87 87 87 ASP ASP A . n A 1 88 ILE 88 88 88 ILE ILE A . n A 1 89 THR 89 89 89 THR THR A . n A 1 90 ALA 90 90 90 ALA ALA A . n A 1 91 SER 91 91 91 SER SER A . n A 1 92 VAL 92 92 92 VAL VAL A . n A 1 93 ASN 93 93 93 ASN ASN A . n A 1 94 CYS 94 94 94 CYS CYS A . n A 1 95 ALA 95 95 95 ALA ALA A . n A 1 96 LYS 96 96 96 LYS LYS A . n A 1 97 LYS 97 97 97 LYS LYS A . n A 1 98 ILE 98 98 98 ILE ILE A . n A 1 99 VAL 99 99 99 VAL VAL A . n A 1 100 SER 100 100 100 SER SER A . n A 1 101 ASP 101 101 101 ASP ASP A . n A 1 102 GLY 102 102 102 GLY GLY A . n A 1 103 ASN 103 103 103 ASN ASN A . n A 1 104 GLY 104 104 104 GLY GLY A . n A 1 105 MET 105 105 105 MET MET A . n A 1 106 ASN 106 106 106 ASN ASN A . n A 1 107 ALA 107 107 107 ALA ALA A . n A 1 108 TRP 108 108 108 TRP TRP A . n A 1 109 VAL 109 109 109 VAL VAL A . n A 1 110 ALA 110 110 110 ALA ALA A . n A 1 111 TRP 111 111 111 TRP TRP A . n A 1 112 ARG 112 112 112 ARG ARG A . n A 1 113 ASN 113 113 113 ASN ASN A . n A 1 114 ARG 114 114 114 ARG ARG A . n A 1 115 CYS 115 115 115 CYS CYS A . n A 1 116 LYS 116 116 116 LYS LYS A . n A 1 117 GLY 117 117 117 GLY GLY A . n A 1 118 THR 118 118 118 THR THR A . n A 1 119 ASP 119 119 119 ASP ASP A . n A 1 120 VAL 120 120 120 VAL VAL A . n A 1 121 GLN 121 121 121 GLN GLN A . n A 1 122 ALA 122 122 122 ALA ALA A . n A 1 123 TRP 123 123 123 TRP TRP A . n A 1 124 ILE 124 124 124 ILE ILE A . n A 1 125 ARG 125 125 125 ARG ARG A . n A 1 126 GLY 126 126 126 GLY GLY A . n A 1 127 CYS 127 127 127 CYS CYS A . n A 1 128 ARG 128 128 128 ARG ARG A . n A 1 129 LEU 129 129 129 LEU LEU A . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email tgonen@g.ucla.edu _pdbx_contact_author.name_first Tamir _pdbx_contact_author.name_last Gonen _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-9254-4069 # 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 B 2 NO3 1 201 201 NO3 NO3 A . C 2 NO3 1 202 202 NO3 NO3 A . D 2 NO3 1 203 203 NO3 NO3 A . E 2 NO3 1 204 204 NO3 NO3 A . F 3 HOH 1 301 1100 HOH HOH A . F 3 HOH 2 302 1017 HOH HOH A . F 3 HOH 3 303 1111 HOH HOH A . F 3 HOH 4 304 1053 HOH HOH A . F 3 HOH 5 305 1082 HOH HOH A . F 3 HOH 6 306 1102 HOH HOH A . F 3 HOH 7 307 1086 HOH HOH A . F 3 HOH 8 308 1079 HOH HOH A . F 3 HOH 9 309 1119 HOH HOH A . F 3 HOH 10 310 1107 HOH HOH A . F 3 HOH 11 311 1080 HOH HOH A . F 3 HOH 12 312 1078 HOH HOH A . F 3 HOH 13 313 1109 HOH HOH A . F 3 HOH 14 314 1083 HOH HOH A . F 3 HOH 15 315 1026 HOH HOH A . F 3 HOH 16 316 1016 HOH HOH A . F 3 HOH 17 317 1037 HOH HOH A . F 3 HOH 18 318 1036 HOH HOH A . F 3 HOH 19 319 1027 HOH HOH A . F 3 HOH 20 320 1004 HOH HOH A . F 3 HOH 21 321 1090 HOH HOH A . F 3 HOH 22 322 1063 HOH HOH A . F 3 HOH 23 323 1071 HOH HOH A . F 3 HOH 24 324 1035 HOH HOH A . F 3 HOH 25 325 1015 HOH HOH A . F 3 HOH 26 326 1005 HOH HOH A . F 3 HOH 27 327 1020 HOH HOH A . F 3 HOH 28 328 1085 HOH HOH A . F 3 HOH 29 329 1084 HOH HOH A . F 3 HOH 30 330 1055 HOH HOH A . F 3 HOH 31 331 1072 HOH HOH A . F 3 HOH 32 332 1025 HOH HOH A . F 3 HOH 33 333 1073 HOH HOH A . F 3 HOH 34 334 1007 HOH HOH A . F 3 HOH 35 335 1023 HOH HOH A . F 3 HOH 36 336 1099 HOH HOH A . F 3 HOH 37 337 1018 HOH HOH A . F 3 HOH 38 338 1009 HOH HOH A . F 3 HOH 39 339 1067 HOH HOH A . F 3 HOH 40 340 1014 HOH HOH A . F 3 HOH 41 341 1002 HOH HOH A . F 3 HOH 42 342 1001 HOH HOH A . F 3 HOH 43 343 1097 HOH HOH A . F 3 HOH 44 344 1021 HOH HOH A . F 3 HOH 45 345 1088 HOH HOH A . F 3 HOH 46 346 1068 HOH HOH A . F 3 HOH 47 347 1108 HOH HOH A . F 3 HOH 48 348 1095 HOH HOH A . F 3 HOH 49 349 1032 HOH HOH A . F 3 HOH 50 350 1042 HOH HOH A . F 3 HOH 51 351 1011 HOH HOH A . F 3 HOH 52 352 1087 HOH HOH A . F 3 HOH 53 353 1051 HOH HOH A . F 3 HOH 54 354 1118 HOH HOH A . F 3 HOH 55 355 1022 HOH HOH A . F 3 HOH 56 356 1010 HOH HOH A . F 3 HOH 57 357 1060 HOH HOH A . F 3 HOH 58 358 1003 HOH HOH A . F 3 HOH 59 359 1092 HOH HOH A . F 3 HOH 60 360 1013 HOH HOH A . F 3 HOH 61 361 1024 HOH HOH A . F 3 HOH 62 362 1040 HOH HOH A . F 3 HOH 63 363 1012 HOH HOH A . F 3 HOH 64 364 1105 HOH HOH A . F 3 HOH 65 365 1089 HOH HOH A . F 3 HOH 66 366 1019 HOH HOH A . F 3 HOH 67 367 1074 HOH HOH A . F 3 HOH 68 368 1039 HOH HOH A . F 3 HOH 69 369 1101 HOH HOH A . F 3 HOH 70 370 1106 HOH HOH A . F 3 HOH 71 371 1030 HOH HOH A . F 3 HOH 72 372 1094 HOH HOH A . F 3 HOH 73 373 1045 HOH HOH A . F 3 HOH 74 374 1113 HOH HOH A . F 3 HOH 75 375 1059 HOH HOH A . F 3 HOH 76 376 1031 HOH HOH A . F 3 HOH 77 377 1058 HOH HOH A . F 3 HOH 78 378 1048 HOH HOH A . F 3 HOH 79 379 1104 HOH HOH A . F 3 HOH 80 380 1093 HOH HOH A . F 3 HOH 81 381 1006 HOH HOH A . F 3 HOH 82 382 1062 HOH HOH A . F 3 HOH 83 383 1056 HOH HOH A . F 3 HOH 84 384 1043 HOH HOH A . F 3 HOH 85 385 1033 HOH HOH A . F 3 HOH 86 386 1075 HOH HOH A . F 3 HOH 87 387 1114 HOH HOH A . F 3 HOH 88 388 1008 HOH HOH A . F 3 HOH 89 389 1034 HOH HOH A . F 3 HOH 90 390 1066 HOH HOH A . F 3 HOH 91 391 1115 HOH HOH A . F 3 HOH 92 392 1064 HOH HOH A . F 3 HOH 93 393 1050 HOH HOH A . F 3 HOH 94 394 1077 HOH HOH A . F 3 HOH 95 395 1052 HOH HOH A . F 3 HOH 96 396 1069 HOH HOH A . F 3 HOH 97 397 1117 HOH HOH A . F 3 HOH 98 398 1103 HOH HOH A . F 3 HOH 99 399 1047 HOH HOH A . F 3 HOH 100 400 1076 HOH HOH A . F 3 HOH 101 401 1110 HOH HOH A . F 3 HOH 102 402 1054 HOH HOH A . F 3 HOH 103 403 1049 HOH HOH A . F 3 HOH 104 404 1038 HOH HOH A . F 3 HOH 105 405 1061 HOH HOH A . F 3 HOH 106 406 1116 HOH HOH A . F 3 HOH 107 407 1041 HOH HOH A . F 3 HOH 108 408 1028 HOH HOH A . F 3 HOH 109 409 1046 HOH HOH A . F 3 HOH 110 410 1081 HOH HOH A . F 3 HOH 111 411 1044 HOH HOH A . F 3 HOH 112 412 1065 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # 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)' 630 ? 1 MORE 4 ? 1 'SSA (A^2)' 6150 ? # _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 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2023-03-15 # _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 ? # _software.citation_id ? _software.classification refinement _software.compiler_name ? _software.compiler_version ? _software.contact_author 'Garib N. Murshudov' _software.contact_author_email garib@mrc-lmb.cam.ac.uk _software.date 2020-24-08 _software.description '(un)restrained refinement or idealisation of macromolecular structures' _software.dependencies ? _software.hardware ? _software.language ? _software.location ? _software.mods ? _software.name REFMAC _software.os ? _software.os_version ? _software.type ? _software.version 5.8.0267 _software.pdbx_ordinal 1 # _pdbx_entry_details.entry_id 7ULY _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _em_3d_fitting.entry_id 7ULY _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value 11.981 _em_3d_fitting.ref_protocol 'AB INITIO MODEL' _em_3d_fitting.ref_space RECIPROCAL _em_3d_fitting.target_criteria 'Maximum likelihood' _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7ULY _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles ? _em_3d_reconstruction.resolution ? _em_3d_reconstruction.resolution_method 'DIFFRACTION PATTERN/LAYERLINES' _em_3d_reconstruction.symmetry_type '3D CRYSTAL' _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 4.5 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name Lysozyme _em_entity_assembly.source NATURAL _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 7ULY _em_image_scans.id 1 _em_image_scans.dimension_height 2048 _em_image_scans.dimension_width 2048 _em_image_scans.frames_per_image ? _em_image_scans.image_recording_id 1 _em_image_scans.sampling_size 28 _em_image_scans.scanner_model ? _em_image_scans.used_frames_per_image ? _em_image_scans.citation_id ? _em_image_scans.number_digital_images ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.details ? # _em_imaging.id 1 _em_imaging.entry_id 7ULY _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure BASIC _em_imaging.c2_aperture_diameter 50.0 _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.mode DIFFRACTION _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_max ? _em_imaging.nominal_defocus_min ? _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum 90 _em_imaging.recording_temperature_minimum 77 _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER' _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 200 _em_sample_support.grid_type 'Quantifoil R2/2' _em_sample_support.method ? _em_sample_support.film_material ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature 277 _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity 95 _em_vitrification.instrument 'LEICA PLUNGER' _em_vitrification.entry_id 7ULY _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7ULY _em_experiment.id 1 _em_experiment.aggregation_state '3D ARRAY' _em_experiment.reconstruction_method CRYSTALLOGRAPHY _em_experiment.entity_assembly_id 1 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OG _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 SER _pdbx_validate_close_contact.auth_seq_id_1 85 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 B _pdbx_validate_close_contact.auth_atom_id_2 OD1 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 ASP _pdbx_validate_close_contact.auth_seq_id_2 87 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.11 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE A ARG 5 ? ? CZ A ARG 5 ? ? NH1 A ARG 5 ? ? 123.54 120.30 3.24 0.50 N 2 1 NE A ARG 112 ? ? CZ A ARG 112 ? ? NH1 A ARG 112 ? ? 123.98 120.30 3.68 0.50 N 3 1 CA A ARG 114 ? ? CB A ARG 114 ? ? CG A ARG 114 ? ? 100.08 113.40 -13.32 2.20 N 4 1 NE A ARG 128 ? ? CZ A ARG 128 ? ? NH1 A ARG 128 ? ? 116.77 120.30 -3.53 0.50 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASN A 37 ? B 34.51 52.34 2 1 ASP A 101 ? ? -91.65 32.75 # _em_3d_crystal_entity.id 1 _em_3d_crystal_entity.image_processing_id 1 _em_3d_crystal_entity.angle_alpha 88.319 _em_3d_crystal_entity.angle_beta 109.095 _em_3d_crystal_entity.angle_gamma 112.075 _em_3d_crystal_entity.length_a 26.42 _em_3d_crystal_entity.length_b 30.72 _em_3d_crystal_entity.length_c 33.01 _em_3d_crystal_entity.space_group_name P1 _em_3d_crystal_entity.space_group_num 1 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type NONE _em_ctf_correction.details ? # _em_diffraction.id 1 _em_diffraction.camera_length 1536 _em_diffraction.imaging_id 1 _em_diffraction.tilt_angle_list ? # _em_diffraction_shell.id 1 _em_diffraction_shell.em_diffraction_stats_id 1 _em_diffraction_shell.fourier_space_coverage 37.64 _em_diffraction_shell.high_resolution 0.87 _em_diffraction_shell.low_resolution 0.90 _em_diffraction_shell.multiplicity 2.1 _em_diffraction_shell.num_structure_factors 2783 _em_diffraction_shell.phase_residual 30 # _em_diffraction_stats.id 1 _em_diffraction_stats.details ? _em_diffraction_stats.image_processing_id 1 _em_diffraction_stats.fourier_space_coverage 87.58 _em_diffraction_stats.high_resolution 0.87 _em_diffraction_stats.num_intensities_measured 569407 _em_diffraction_stats.num_structure_factors 64974 _em_diffraction_stats.overall_phase_error 30 _em_diffraction_stats.overall_phase_residual ? _em_diffraction_stats.phase_error_rejection_criteria None _em_diffraction_stats.r_merge 0.236 _em_diffraction_stats.r_sym 0.073 # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 0.0144 # _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 9031 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Gallus gallus' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details 'Binned by 2' # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 0.001 _em_image_recording.average_exposure_time 0.5 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'FEI FALCON IV (4k x 4k)' _em_image_recording.num_diffraction_images 840 _em_image_recording.num_grids_imaged 1 _em_image_recording.num_real_images 1 _em_image_recording.avg_electron_dose_per_subtomogram ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'IMAGE ACQUISITION' ? ? ? ? ? 1 2 MASKING ? ? ? ? ? ? 3 'CTF CORRECTION' ? ? ? 1 ? ? 4 'LAYERLINE INDEXING' ? ? ? ? ? ? 5 'DIFFRACTION INDEXING' ? ? ? ? ? ? 6 'MODEL FITTING' ? ? ? ? 1 ? 7 OTHER ? ? ? ? ? ? 8 'MODEL REFINEMENT' ? REFMAC 5.8.0267 ? 1 ? 9 'MOLECULAR REPLACEMENT' ? ? ? 1 ? ? 10 'LATTICE DISTORTION CORRECTION' ? ? ? 1 ? ? 11 'SYMMETRY DETERMINATION' ? ? ? 1 ? ? 12 'CRYSTALLOGRAPHY MERGING' ? AIMLESS ? 1 ? ? 13 RECONSTRUCTION ? REFMAC 5.8.0267 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 10 _em_specimen.details 'Protein crystal lamellae' _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Howard Hughes Medical Institute (HHMI)' 'United States' ? 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' GM136508 2 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NITRATE ION' NO3 3 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #