data_8RC7

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8RC7
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8RC7
_pdbx_vrpt_summary.PDB_deposition_date         2023-12-06
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2024-03-06
_pdbx_vrpt_summary.report_creation_date        2024-02-26:15:40
_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      "Gramicidin S"  
2  non-polymer  UREA  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  0.98  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   99.76    1241  0.90  1.06  
 3  1  2  100.00  138981     ?     ?  
 4  2  2  100.00    1159  0.90  1.06  
 5  1  3  100.00  138945     ?     ?  
 6  2  3  100.00    1161  0.90  1.06  
 7  1  4  100.00  127900     ?     ?  
 8  2  4  100.00    1132  0.90  1.06  
 9  1  5   98.77  130704     ?     ?  
10  2  5   56.60    1166  0.90  1.06  
#
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  D  100.00  
2  4  2  A  1  1  D  100.00  
3  5  3  A  1  1  D  100.00  
4  6  3  A  1  1  D  100.00  
5  7  4  A  1  1  D  100.00  
6  8  4  A  1  1  D  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     D
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      1.32
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.72
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   47
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  56
#
_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                   101
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 47
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.72
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                56
_pdbx_vrpt_summary_geometry.angles_RMSZ                    1.32
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 111.506
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            69.915
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         8.390
_pdbx_vrpt_summary_diffraction.I_over_sigma              60.17(0.98A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        4028
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.087
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.455
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.463
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.289
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.979
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.090
_pdbx_vrpt_summary_diffraction.DCC_R                     0.15
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.15
_pdbx_vrpt_summary_diffraction.EDS_R                     0.14
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.98
_pdbx_vrpt_summary_diffraction.EDS_res_low               22.34
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[8.407,8.407,8.351,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.007
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 17.23% of the height of the origin peak. No significant pseudotranslation is detected."
_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         80.74
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      205
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.09
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       0.98
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        22.34
_pdbx_vrpt_summary_diffraction.PDB_R                     0.14
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.13
#
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
_pdbx_vrpt_model_instance.count_mogul_bond_outliers
 1  1  1  A   1  VAL  D    1  A  ?        ?  
 2  1  1  A   1  VAL  D    1  B  ?        ?  
 3  1  1  A   2  ORN  D    2  .  ?        1  
 4  1  1  A   3  LEU  D    3  .  ?        ?  
 5  1  1  A   4  DPN  D    4  .  ?        ?  
 6  1  1  A   5  PRO  D    5  .  ?        ?  
 7  1  1  A   6  VAL  D    6  .  ?        ?  
 8  1  1  A   7  ORN  D    7  .  ?        ?  
 9  1  1  A   8  LEU  D    8  .  ?        ?  
10  1  1  A   9  DPN  D    9  .  ?        ?  
11  1  1  A  10  PRO  D   10  .  ?        ?  
12  1  2  B   .  URE  D  101  .  ?        ?  
13  1  3  C   .  HOH  D  201  .  ?        ?  
14  1  3  C   .  HOH  D  202  .  ?        ?  
15  1  3  C   .  HOH  D  203  .  ?        ?  
16  1  3  C   .  HOH  D  204  .  ?        ?  
17  1  3  C   .  HOH  D  205  .  ?        ?  
18  1  3  C   .  HOH  D  206  .  ?        ?  
19  1  3  C   .  HOH  D  207  .  ?        ?  
20  1  3  C   .  HOH  D  208  .  ?        ?  
21  1  3  C   .  HOH  D  209  .  ?        ?  
#
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  t             ?      ?  ?           9   6.540     6  0.76     7  2.05  molprobity  1.000  
 2   2  t             ?      ?  ?           9   6.540     6  0.76     7  2.05  molprobity  1.000  
 3   3  ?             ?      ?  ?           9   9.460     6  1.01     2  0.49  mogul       1.000  
 4   4  mp       -122.5   93.5  Favored    11   9.100     7  0.73     8  1.21  molprobity  1.000  
 5   5  ?             ?      ?  ?           8   9.540     ?     ?     ?     ?  ?           1.000  
 6   6  Cg_endo   -80.7   -2.1  Favored     7   8.780     8  0.86    11  1.07  molprobity  1.000  
 7   7  m        -124.2  156.6  Favored     9   7.700     6  0.41     7  0.92  molprobity  1.000  
 8   8  ?             ?      ?  ?           9  12.710     6  0.72     2  0.61  mogul       1.000  
 9   9  mt       -140.1  121.3  Favored    11   9.580     7  0.60     8  0.83  molprobity  1.000  
10  10  ?             ?      ?  ?           8   7.820     ?     ?     ?     ?  ?           1.000  
11  11  Cg_endo       ?      ?  ?           7   6.900     7  0.75     8  0.56  molprobity  1.000  
12  12  ?             ?      ?  ?           4   7.730     3  0.38     3  0.49  mogul       0.500  
13  13  ?             ?      ?  ?           ?  12.160     ?     ?     ?     ?  ?           1.000  
14  14  ?             ?      ?  ?           ?  12.770     ?     ?     ?     ?  ?           1.000  
15  15  ?             ?      ?  ?           ?  29.500     ?     ?     ?     ?  ?           1.000  
16  16  ?             ?      ?  ?           ?  24.510     ?     ?     ?     ?  ?           1.000  
17  17  ?             ?      ?  ?           ?  31.030     ?     ?     ?     ?  ?           1.000  
18  18  ?             ?      ?  ?           ?  13.010     ?     ?     ?     ?  ?           0.500  
19  19  ?             ?      ?  ?           ?  35.220     ?     ?     ?     ?  ?           0.500  
20  20  ?             ?      ?  ?           ?  33.600     ?     ?     ?     ?  ?           1.000  
21  21  ?             ?      ?  ?           ?  20.940     ?     ?     ?     ?  ?           0.500  
#
_pdbx_vrpt_instance_mogul_bond_outliers.ordinal      1
_pdbx_vrpt_instance_mogul_bond_outliers.instance_id  3
_pdbx_vrpt_instance_mogul_bond_outliers.atom_1       CB
_pdbx_vrpt_instance_mogul_bond_outliers.atom_2       CA
_pdbx_vrpt_instance_mogul_bond_outliers.obsval       1.50
_pdbx_vrpt_instance_mogul_bond_outliers.mean         1.53
_pdbx_vrpt_instance_mogul_bond_outliers.numobs       56
_pdbx_vrpt_instance_mogul_bond_outliers.stdev        0.01
_pdbx_vrpt_instance_mogul_bond_outliers.Zscore       -2.01
_pdbx_vrpt_instance_mogul_bond_outliers.mindiff      0.00
#
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  14  0.984  0.063  -0.271  
 2   2  14  0.984  0.063  -0.271  
 3   3   8  0.975  0.068       ?  
 4   4   8  0.979  0.070  -0.096  
 5   5  11  0.970  0.059       ?  
 6   6   7  0.972  0.059  -0.324  
 7   7   7  0.983  0.048  -0.780  
 8   8   8  0.979  0.068       ?  
 9   9   8  0.985  0.058  -0.505  
10  10  11  0.987  0.047       ?  
11  11   7  0.984  0.044  -0.704  
12  12   4  0.990  0.060       ?  
13  13   1  0.968  0.062       ?  
14  14   1  0.934  0.076       ?  
15  15   1  0.721  0.245       ?  
16  16   1  0.860  0.079       ?  
17  17   1  0.793  0.180       ?  
18  18   1  0.959  0.133       ?  
19  19   1  0.830  0.157       ?  
20  20   1  0.706  0.165       ?  
21  21   1  0.873  0.187       ?  
#
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        "1.8.4, CSD as541be (2020)"                                           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  
##
