data_6GQC

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6GQC
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6GQC
_pdbx_vrpt_summary.PDB_deposition_date         2018-06-07
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-01-17
_pdbx_vrpt_summary.report_creation_date        2024-01-07:07:52
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "Phenol-soluble modulin alpha 3 peptide"  
2  non-polymer  "SODIUM ION"  
3  non-polymer  "CHLORIDE ION"  
4  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  2  
D  3  
E  4  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.4  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  141614     ?     ?  
 2  2  1  100.00    1812  1.40  1.40  
 3  1  2  100.00  138981     ?     ?  
 4  2  2  100.00    1763  1.40  1.40  
 5  1  3   22.41  138945     ?     ?  
 6  2  3    2.72    1762  1.40  1.40  
 7  1  4   32.89  127900     ?     ?  
 8  2  4   33.21    1674  1.40  1.40  
 9  1  5   89.99  130704     ?     ?  
10  2  5   60.60    1714  1.40  1.40  
#
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   24.16  
4  6  3  A  1  1  A    3.18  
5  7  4  A  1  1  A   32.89  
6  8  4  A  1  1  A   33.21  
#
_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      0.72
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.54
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   198
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  260
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       5.26
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   206
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 198
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.54
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                260
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.72
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 328.659
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            44.525
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         15.528
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.96(1.40A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3478
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.076
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.438
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.469
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.303
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.970
_pdbx_vrpt_summary_diffraction.DCC_R                     0.15
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.19
_pdbx_vrpt_summary_diffraction.EDS_R                     0.17
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.40
_pdbx_vrpt_summary_diffraction.EDS_res_low               14.67
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[15.527,16.164,15.078,0.000,1.277,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.070
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 25.30 % 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 3.2550e-03. 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          0
_pdbx_vrpt_summary_diffraction.data_completeness         99.37
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      348
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.01
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     4.55
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.40
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        14.67
_pdbx_vrpt_summary_diffraction.PDB_R                     0.15
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.19
#
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  MET  A    1  .  ?     
 2  1  1  A   2  GLU  A    2  .  ?     
 3  1  1  A   3  PHE  A    3  .  ?     
 4  1  1  A   4  VAL  A    4  .  ?     
 5  1  1  A   5  ALA  A    5  .  ?     
 6  1  1  A   6  LYS  A    6  .  ?     
 7  1  1  A   7  LEU  A    7  A  ?     
 8  1  1  A   7  LEU  A    7  B  ?     
 9  1  1  A   8  PHE  A    8  .  ?     
10  1  1  A   9  LYS  A    9  .  ?     
11  1  1  A  10  PHE  A   10  .  ?     
12  1  1  A  11  PHE  A   11  .  ?     
13  1  1  A  12  LYS  A   12  .  ?     
14  1  1  A  13  ASP  A   13  .  ?     
15  1  1  A  14  LEU  A   14  .  ?     
16  1  1  A  15  LEU  A   15  .  ?     
17  1  1  A  16  ALA  A   16  .  ?     
18  1  1  A  17  LYS  A   17  .  ?     
19  1  1  A  18  PHE  A   18  .  ?     
20  1  1  A  19  LEU  A   19  .  ?     
21  1  1  A  20  GLY  A   20  .  ?     
22  1  1  A  21  ASN  A   21  .  ?     
23  1  1  A  22  ASN  A   22  .  ?     
24  1  2  B   .  NA   A  101  .  ?     
25  1  2  C   .  NA   A  102  .  ?     
26  1  3  D   .  CL   A  103  .  ?     
27  1  4  E   .  HOH  A  201  .  ?     
28  1  4  E   .  HOH  A  202  .  ?     
#
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.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  ttm           ?      ?  ?          11  25.270     8  0.56    10  0.76  molprobity  1.000  
 2   2  pm0       -62.0  157.1  Favored     6  16.840     9  0.52    12  0.89  molprobity  1.000  
 3   3  t80       -64.8  -43.5  Favored     9  15.160    12  0.43    16  0.60  molprobity  1.000  
 4   4  t         -64.2  -39.0  Favored     9  15.840     7  0.59    10  0.57  molprobity  1.000  
 5   5  ?         -63.4  -41.8  Favored     5  14.270     5  0.27     7  0.35  molprobity  1.000  
 6   6  mtmt      -59.5  -42.6  Favored    13  19.530     9  0.34    11  0.68  molprobity  1.000  
 7   7  tp        -69.0  -46.4  Favored    11  14.040     8  0.48    11  0.73  molprobity  1.000  
 8   8  tp        -69.0  -46.4  Favored    11  14.040     8  0.48    11  0.73  molprobity  1.000  
 9   9  m-30      -58.7  -45.1  Favored     8  13.370    12  0.51    16  0.97  molprobity  1.000  
10  10  tttp      -58.5  -42.0  Favored    13  17.440     9  0.51    11  0.70  molprobity  1.000  
11  11  t80       -57.6  -45.9  Favored     9  13.290    12  0.73    16  0.53  molprobity  1.000  
12  12  m-85      -73.3  -34.4  Favored     9  11.420    12  0.60    16  0.87  molprobity  1.000  
13  13  ttpp      -67.5  -41.7  Favored    13  20.450     9  0.55    11  0.68  molprobity  0.933  
14  14  m-20      -65.2  -38.5  Favored     4  20.990     8  0.64    11  0.96  molprobity  1.000  
15  15  tp        -63.3  -45.4  Favored    11  16.290     8  0.39    11  0.85  molprobity  1.000  
16  16  tp        -60.4  -37.9  Favored    11  15.950     8  0.58    11  0.54  molprobity  1.000  
17  17  ?         -63.8  -24.3  Favored     5  13.200     5  0.50     7  0.67  molprobity  1.000  
18  18  mmtp      -66.8  -23.6  Favored    13  19.950     9  0.54    11  0.38  molprobity  1.000  
19  19  m-85      -95.4  -40.5  Favored     9  15.590    12  0.90    16  0.55  molprobity  1.000  
20  20  mt       -108.3   -7.8  Favored    11  15.300     8  0.26    11  0.81  molprobity  1.000  
21  21  ?          95.2  176.6  Favored     3  15.960     4  0.41     5  0.64  molprobity  1.000  
22  22  OUTLIER   -74.4  -30.8  Favored     6  32.960     8  0.40    11  0.87  molprobity  1.000  
23  23  m120          ?      ?  ?           6  32.950     8  0.49     8  0.55  molprobity  1.000  
24  24  ?             ?      ?  ?           ?  43.610     ?     ?     ?     ?  ?           1.000  
25  25  ?             ?      ?  ?           ?  43.110     ?     ?     ?     ?  ?           1.000  
26  26  ?             ?      ?  ?           ?  53.660     ?     ?     ?     ?  ?           1.000  
27  27  ?             ?      ?  ?           ?  25.890     ?     ?     ?     ?  ?           1.000  
28  28  ?             ?      ?  ?           ?  23.410     ?     ?     ?     ?  ?           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
 1   1   8  0.960  0.095   0.114  
 2   2   9  0.954  0.067  -0.788  
 3   3  11  0.983  0.047  -1.089  
 4   4   7  0.976  0.058  -0.841  
 5   5   5  0.981  0.046  -0.890  
 6   6   9  0.946  0.095  -0.422  
 7   7  16  0.968  0.111   0.666  
 8   8  16  0.968  0.111   0.666  
 9   9  11  0.971  0.059  -0.708  
10  10   9  0.963  0.075  -0.757  
11  11  11  0.977  0.059  -0.708  
12  12  11  0.983  0.079  -0.073  
13  13   9  0.957  0.117  -0.054  
14  14   8  0.910  0.103   0.099  
15  15   8  0.980  0.060  -0.870  
16  16   8  0.962  0.073  -0.479  
17  17   5  0.977  0.067  -0.375  
18  18   9  0.933  0.131   0.181  
19  19  11  0.955  0.070  -0.359  
20  20   8  0.953  0.088  -0.027  
21  21   4  0.978  0.059  -0.476  
22  22   8  0.908  0.188   1.831  
23  23   9  0.808  0.212   2.291  
24  24   1  0.945  0.315       ?  
25  25   1  0.921  0.438       ?  
26  26   1  0.980  0.230       ?  
27  27   1  0.989  0.077       ?  
28  28   1  0.989  0.133       ?  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  mogul        unknown                                                               Y  
3  eds          2.36                                                                  Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
