data_5MAS

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.068
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  5MAS
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    5MAS
_pdbx_vrpt_summary.PDB_deposition_date         2016-11-04
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2025-04-09
_pdbx_vrpt_summary.report_creation_date        2025-04-01:23:34
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds_mogul,validation_schema,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  "Bergofungin A"  
2  water    water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  0.84  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   99.86    1413  0.68  1.00  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1333  0.68  1.00  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1334  0.68  1.00  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1270  0.70  1.00  
 9  1  5   99.88  164625     ?     ?  
10  2  5   89.21    1273  0.70  1.00  
#
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      0.68
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.64
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   34
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  44
#
_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                   118
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 34
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.64
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                44
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.68
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            127.145
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         3.262
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.31(0.84A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        12250
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.259
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.449
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.302
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.986
_pdbx_vrpt_summary_diffraction.twin_fraction             -h-2*l,-k,l:0.027
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1025
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1173
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1055
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.84
_pdbx_vrpt_summary_diffraction.EDS_res_low               21.37
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[3.647,3.051,3.135,0.000,0.129,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.182
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 36.42 % 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 5.0085e-04."
_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         79.93
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      393
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.38
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       0.84
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        30.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.1040
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.1310
_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
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
 1  1  1  A   1  ACE  A    0  .  ?        ?     ?  
 2  1  1  A   2  VAL  A    1  .  ?        ?     ?  
 3  1  1  A   3  AIB  A    2  .  ?        ?     ?  
 4  1  1  A   4  AIB  A    3  .  ?        ?     ?  
 5  1  1  A   5  AIB  A    4  .  ?        ?     ?  
 6  1  1  A   6  VAL  A    5  .  ?        ?     ?  
 7  1  1  A   7  GLY  A    6  .  ?        ?     ?  
 8  1  1  A   8  LEU  A    7  .  ?        ?     ?  
 9  1  1  A   9  AIB  A    8  .  ?        ?     ?  
10  1  1  A  10  AIB  A    9  .  ?        ?     ?  
11  1  1  A  11  HYP  A   10  .  ?        1     ?  
12  1  1  A  12  GLN  A   11  .  ?        ?     ?  
13  1  1  A  13  DIV  A   12  .  ?        ?     ?  
14  1  1  A  14  HYP  A   13  .  ?        1     ?  
15  1  1  A  15  AIB  A   14  .  ?        ?     2  
16  1  1  A  16  PHL  A   15  .  ?        ?     ?  
17  1  2  B   .  HOH  A  101  .  ?        ?     ?  
#
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  ?           ?      ?  ?           3  5.230     1  0.02     2  0.58  molprobity  1.000  
 2   2  t      -121.0  -71.2  Allowed     9  4.500     6  0.52     7  0.83  molprobity  1.000  
 3   3  ?           ?      ?  ?           7  4.080     1  1.64     2  0.66  mogul       1.000  
 4   4  ?           ?      ?  ?           7  4.560     1  0.95     2  0.42  mogul       1.000  
 5   5  ?           ?      ?  ?           7  4.440     1  1.02     2  0.47  mogul       1.000  
 6   6  t       -59.9  -44.9  Favored     9  4.250     7  0.90    10  0.82  molprobity  1.000  
 7   7  ?       -62.5  -40.5  Favored     3  3.540     4  0.47     5  0.60  molprobity  1.000  
 8   8  mt      -72.5  -37.9  Favored    11  4.820     7  0.50     8  0.63  molprobity  1.000  
 9   9  ?           ?      ?  ?           7  3.840     1  1.18     2  0.35  mogul       1.000  
10  10  ?           ?      ?  ?           7  3.350     1  1.05     2  0.38  mogul       1.000  
11  11  ?           ?      ?  ?           7  3.150     6  0.64     5  1.20  mogul       1.000  
12  12  mm-40   -83.6  -17.3  Favored     8  3.550     8  0.65     9  0.50  molprobity  1.000  
13  13  ?           ?      ?  ?           8  4.800     2  0.81     3  0.50  mogul       1.000  
14  14  ?           ?      ?  ?           7  4.380     6  0.63     5  1.08  mogul       1.000  
15  15  ?           ?      ?  ?           7  4.580     1  1.64     2  0.67  mogul       1.000  
16  16  ?           ?      ?  ?          11  4.390    11  0.63    11  0.72  mogul       1.000  
17  17  ?           ?      ?  ?           ?  1.780     ?     ?     ?     ?  ?           0.500  
#
loop_
_pdbx_vrpt_instance_mogul_angle_outliers.ordinal
_pdbx_vrpt_instance_mogul_angle_outliers.instance_id
_pdbx_vrpt_instance_mogul_angle_outliers.atom_1
_pdbx_vrpt_instance_mogul_angle_outliers.atom_2
_pdbx_vrpt_instance_mogul_angle_outliers.atom_3
_pdbx_vrpt_instance_mogul_angle_outliers.obsval
_pdbx_vrpt_instance_mogul_angle_outliers.mean
_pdbx_vrpt_instance_mogul_angle_outliers.numobs
_pdbx_vrpt_instance_mogul_angle_outliers.stdev
_pdbx_vrpt_instance_mogul_angle_outliers.Zscore
_pdbx_vrpt_instance_mogul_angle_outliers.mindiff
1  11  O  C  CA  119.52  124.78  82  2.62  -2.01  0.37  
2  14  O  C  CA  118.87  124.78  82  2.62  -2.25  0.46  
#
loop_
_pdbx_vrpt_instance_mogul_torsion_outliers.ordinal
_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_1
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_2
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_3
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_4
_pdbx_vrpt_instance_mogul_torsion_outliers.obsval
_pdbx_vrpt_instance_mogul_torsion_outliers.mean
_pdbx_vrpt_instance_mogul_torsion_outliers.numobs
_pdbx_vrpt_instance_mogul_torsion_outliers.stdev
_pdbx_vrpt_instance_mogul_torsion_outliers.mindiff
_pdbx_vrpt_instance_mogul_torsion_outliers.local_density
1  15  O  C  CA  CB1  -80.69  47.49  42  21.02  11.04  0.00  
2  15  O  C  CA  CB2   39.18  55.67  42  26.27   7.90  2.38  
#
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   6  0.994  0.024       ?  0.698  33.330  
 2   2  16  0.996  0.019  -1.363  0.691  14.290  
 3   3  13  0.995  0.022       ?  0.721  33.330  
 4   4  13  0.994  0.025       ?  0.702  16.670  
 5   5  13  0.995  0.022       ?  0.749  16.670  
 6   6  16  0.994  0.025  -1.094  0.713  28.570  
 7   7   7  0.995  0.021  -0.918  0.718  50.000  
 8   8  19  0.995  0.025  -1.174  0.674  12.500  
 9   9  13  0.997  0.018       ?  0.708  16.670  
10  10  13  0.996  0.018       ?  0.693  16.670  
11  11  15  0.996  0.021       ?  0.689  37.500  
12  12  17  0.996  0.019  -1.201  0.735  33.330  
13  13  16  0.995  0.023       ?  0.693  14.290  
14  14  15  0.996  0.022       ?  0.703  25.000  
15  15  13  0.995  0.025       ?  0.682  16.670  
16  16  23  0.994  0.026       ?  0.688  18.180  
17  17   1  0.977  0.060       ?  0.749   0.000  
#
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          3.0                                                                   Y  
4  dcc          '"2.31  (2025-03-10))"'                                               Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
