data_9GJ3

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.070
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_entry.id  9GJ3
#
_entity.id                        1
_entity.type                      polymer
_entity.src_method                syn
_entity.pdbx_description          "Peptide LYIQNY"
_entity.formula_weight            812.910
_entity.pdbx_number_of_molecules  1
_entity.pdbx_ec                   ?
_entity.pdbx_mutation             ?
_entity.pdbx_fragment             ?
_entity.details                   ?
#
_struct_asym.id                           A
_struct_asym.pdbx_blank_PDB_chainid_flag  ?
_struct_asym.pdbx_modified                N
_struct_asym.entity_id                    1
_struct_asym.details                      ?
#
_pdbx_vrpt_database.id             PDB
_pdbx_vrpt_database.code           9GJ3
_pdbx_vrpt_database.extended_code  pdb_00009gj3
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    9GJ3
_pdbx_vrpt_summary.extended_entry_id           pdb_00009gj3
_pdbx_vrpt_summary.PDB_deposition_date         2024-08-21
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2025-07-09
_pdbx_vrpt_summary.report_creation_date        2025-06-30:15:50
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,validation_schema,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
_pdbx_vrpt_entity.id           1
_pdbx_vrpt_entity.type         polymer
_pdbx_vrpt_entity.description  "Peptide LYIQNY"
#
_pdbx_vrpt_asym.label_asym_id  A
_pdbx_vrpt_asym.entity_id      1
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.5  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
4  RSRZ_outliers_percent         
5  R_value_R_free                
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
 1  1  1   99.96  180529     ?     ?  
 2  2  1   99.95    4048  1.50  1.50  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    3970  1.50  1.50  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    3967  1.50  1.50  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    3718  1.50  1.50  
 9  1  5   99.95  164625     ?     ?  
10  2  5  100.00    3717  1.50  1.50  
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
1  3  2  A  1  1  A  100.00  
2  4  2  A  1  1  A  100.00  
3  5  3  A  1  1  A  100.00  
4  6  3  A  1  1  A  100.00  
5  7  4  A  1  1  A  100.00  
6  8  4  A  1  1  A  100.00  
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     A
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      0.73
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.49
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   59
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  78
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       0.00
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   56
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 59
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.49
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                78
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.73
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            61.824
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         7.074
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.06(1.40A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        982
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.219
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.431
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.279
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.988
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1004
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1097
_pdbx_vrpt_summary_diffraction.EDS_R                     0.0988
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.50
_pdbx_vrpt_summary_diffraction.EDS_res_low               21.16
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[8.637,7.622,3.376,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.804
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 39.89 % of the origin peak, indicating pseudo-translational symmetry.  The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 2.9682e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio.  See the relevant section of the logfile for more details."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         0
_pdbx_vrpt_summary_diffraction.centric_outliers          1
_pdbx_vrpt_summary_diffraction.data_completeness         92.33
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      762
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.09
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.50
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        21.16
_pdbx_vrpt_summary_diffraction.PDB_R                     0.1014
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.1097
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.11
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.003 (Gargrove)"
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
1  1  1  A  1  LEU  A  1  .  ?     
2  1  1  A  2  TYR  A  2  .  ?     
3  1  1  A  3  ILE  A  3  .  ?     
4  1  1  A  4  GLN  A  4  .  ?     
5  1  1  A  5  ASN  A  5  .  ?     
6  1  1  A  6  TYR  A  6  .  ?     
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.flippable_sidechain
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.OWAB
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
_pdbx_vrpt_model_instance_geometry.average_occupancy
1  1  tt         ?      ?  ?           ?  13  14.010   8  0.67  11  0.77  molprobity  1.000  
2  2  t80   -135.4  124.8  Favored     ?   9   3.970  13  0.44  18  0.94  molprobity  1.000  
3  3  mt    -119.9  124.9  Favored     ?  11   4.920   8  0.39  11  0.43  molprobity  1.000  
4  4  mt0   -118.5  115.0  Favored     1   8   3.820   9  0.54  12  0.79  molprobity  1.000  
5  5  t0    -122.5  126.3  Favored     ?   6   5.800   8  0.54  11  0.74  molprobity  1.000  
6  6  m-80       ?      ?  ?           ?   9   5.770  13  0.41  15  0.51  molprobity  1.000  
#
loop_
_pdbx_vrpt_model_instance_density.ordinal
_pdbx_vrpt_model_instance_density.instance_id
_pdbx_vrpt_model_instance_density.natoms_eds
_pdbx_vrpt_model_instance_density.RSRCC
_pdbx_vrpt_model_instance_density.RSR
_pdbx_vrpt_model_instance_density.RSRZ
_pdbx_vrpt_model_instance_density.EDIAm
_pdbx_vrpt_model_instance_density.OPIA
1  1  21  0.973  0.051  -0.545  0.668   50.000  
2  2  21  0.978  0.033  -0.986  0.868  100.000  
3  3  19  0.977  0.038  -0.972  0.828   50.000  
4  4  17  0.980  0.033  -1.232  0.883  100.000  
5  5  14  0.986  0.030  -1.114  0.902   87.500  
6  6  22  0.976  0.033  -0.986  0.859   90.910  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity           "4-5-2 with Phenix2.0rc1"                                             Y  
2  eds                  3.0                                                                   Y  
3  dcc                  '"2.31  (2025-03-10))"'                                               Y  
4  xtriage              2.0rc1                                                                Y  
5  percentiles          "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
6  validation-pipeline  2.44                                                                  Y  
##
