data_7TML

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.066
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7TML
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7TML
_pdbx_vrpt_summary.PDB_deposition_date         2022-01-19
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2024-09-25
_pdbx_vrpt_summary.report_creation_date        2024-09-17:14:09
_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      "bipyridyl-conjugated helical peptide"  
2  non-polymer  iodobenzene  
3  non-polymer  ACETONITRILE  
4  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  0.93  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   32.91  180529     ?     ?  
 2  2  1   23.94    1203  0.88  1.00  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1135  0.88  1.00  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1136  0.88  1.00  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1076  0.88  1.00  
 9  1  5   67.79  164625     ?     ?  
10  2  5    2.13    1077  0.88  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      0.52
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.33
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   44
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  57
#
_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                     7.72
_pdbx_vrpt_summary_geometry.num_H_reduce                   97
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 44
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.33
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                57
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.52
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            0.000
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         4.244
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.20(0.81A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        10201
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.000
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.461
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.300
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.955
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1836
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.2219
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1861
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.93
_pdbx_vrpt_summary_diffraction.EDS_res_low               8.78
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[5.472,4.363,3.092,0.000,0.155,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.552
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 43.62 % 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 1.7181e-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         3
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         98.37
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      324
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.62
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       0.93
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        8.78
_pdbx_vrpt_summary_diffraction.PDB_R                     0.18
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.22
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.11
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.002 (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_clashes
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
 1  1  1  A   1  I6W  A    1  A  ?        ?     ?  
 2  1  1  A   1  I6W  A    1  B  ?        ?     ?  
 3  1  1  A   2  LEU  A    2  .  ?        ?     ?  
 4  1  1  A   3  AIB  A    3  .  ?        ?     ?  
 5  1  1  A   4  ALA  A    4  .  ?        ?     ?  
 6  1  1  A   5  AIB  A    5  .  ?        ?     ?  
 7  1  1  A   6  LEU  A    6  .  ?        ?     ?  
 8  1  1  A   7  AIB  A    7  .  ?        ?     2  
 9  1  1  A   8  GLN  A    8  .  ?        ?     ?  
10  1  1  A   9  AIB  A    9  .  ?        ?     ?  
11  1  1  A  10  LEU  A   10  A  ?        1     ?  
12  1  1  A  10  LEU  A   10  B  ?        ?     ?  
13  1  1  A  11  I77  A   11  A  ?        2     ?  
14  1  1  A  11  I77  A   11  B  ?        ?     ?  
15  1  2  B   .  PIH  A  201  A  ?        ?     ?  
16  1  2  B   .  PIH  A  201  B  ?        ?     ?  
17  1  3  C   .  CCN  A  202  .  ?        ?     ?  
18  1  4  D   .  HOH  A  301  .  ?        1     ?  
19  1  4  D   .  HOH  A  302  .  ?        ?     ?  
20  1  4  D   .  HOH  A  303  .  ?        ?     ?  
21  1  4  D   .  HOH  A  304  .  ?        ?     ?  
22  1  4  D   .  HOH  A  305  .  ?        ?     ?  
23  1  4  D   .  HOH  A  306  .  ?        ?     ?  
24  1  4  D   .  HOH  A  307  .  ?        ?     ?  
25  1  4  D   .  HOH  A  308  .  ?        ?     ?  
#
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  ?         ?      ?  ?           ?   4.130     ?     ?     ?     ?  ?           0.510  
 2   2  ?         ?      ?  ?           ?   4.130     ?     ?     ?     ?  ?           0.510  
 3   3  tp        ?      ?  ?          10   8.030     7  0.38     8  0.44  molprobity  1.000  
 4   4  ?         ?      ?  ?           7   4.180     1  1.18     0     ?  mogul       1.000  
 5   5  ?     -59.7  -44.5  Favored     5   5.350     4  0.36     4  0.39  molprobity  1.000  
 6   6  ?         ?      ?  ?           7   4.180     1  1.24     0     ?  mogul       1.000  
 7   7  mt    -86.5  -43.7  Favored    11   5.550     7  0.20     8  0.44  molprobity  1.000  
 8   8  ?         ?      ?  ?           7   4.160     1  1.15     0     ?  mogul       1.000  
 9   9  pt20  -55.8  -24.9  Favored     8   3.240     8  0.48     9  0.21  molprobity  1.000  
10  10  ?         ?      ?  ?           7   3.630     1  0.99     0     ?  mogul       1.000  
11  11  mt        ?      ?  ?          11   2.230     7  0.27     8  0.56  molprobity  0.500  
12  12  mt        ?      ?  ?          11   2.230     7  0.27     8  0.56  molprobity  0.500  
13  13  ?         ?      ?  ?           ?   2.490     ?     ?     ?     ?  ?           0.500  
14  14  ?         ?      ?  ?           ?   2.490     ?     ?     ?     ?  ?           0.500  
15  15  ?         ?      ?  ?           5   1.990     7  0.33     8  0.74  mogul       0.340  
16  16  ?         ?      ?  ?           5   1.990     7  0.23     8  0.54  mogul       0.340  
17  17  ?         ?      ?  ?           3   6.280     2  0.82     1  0.57  mogul       1.000  
18  18  ?         ?      ?  ?           ?   5.890     ?     ?     ?     ?  ?           1.000  
19  19  ?         ?      ?  ?           ?   1.230     ?     ?     ?     ?  ?           1.000  
20  20  ?         ?      ?  ?           ?   8.270     ?     ?     ?     ?  ?           1.000  
21  21  ?         ?      ?  ?           ?   1.760     ?     ?     ?     ?  ?           1.000  
22  22  ?         ?      ?  ?           ?  13.150     ?     ?     ?     ?  ?           1.000  
23  23  ?         ?      ?  ?           ?  23.520     ?     ?     ?     ?  ?           1.000  
24  24  ?         ?      ?  ?           ?  20.620     ?     ?     ?     ?  ?           1.000  
25  25  ?         ?      ?  ?           ?  10.620     ?     ?     ?     ?  ?           1.000  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
1  11  O    1  0.48  2.32  
2  13  O16  2  0.83  1.95  
3  13  O16  1  0.48  2.32  
4  18  O    2  0.83  1.95  
#
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  8  O  C  CA  CB1   36.96  53.61  50  27.97  5.68  2.00  
2  8  O  C  CA  CB2  -80.44  46.33  50  21.80  7.10  2.00  
#
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
_pdbx_vrpt_model_instance_density.EDIAm
_pdbx_vrpt_model_instance_density.OPIA
 1   1  59  0.912  0.092       ?  0.520   18.750  
 2   2  59  0.912  0.092       ?  0.520   18.750  
 3   3  18  0.977  0.046  -0.281  0.875   75.000  
 4   4  13  0.992  0.028       ?  0.879   83.330  
 5   5  10  0.990  0.031  -0.667  0.867   60.000  
 6   6  13  0.992  0.028       ?  0.814   50.000  
 7   7  19  0.982  0.045  -0.323  0.927  100.000  
 8   8  13  0.986  0.032       ?  0.865   83.330  
 9   9  17  0.993  0.023  -1.098  0.837   66.670  
10  10  13  0.990  0.026       ?  0.888  100.000  
11  11  38  0.948  0.050  -0.111  0.820   75.000  
12  12  38  0.948  0.050  -0.111  0.820   75.000  
13  13  56  0.901  0.094       ?  0.474   12.350  
14  14  56  0.901  0.094       ?  0.474   12.350  
15  15  24  0.975  0.128       ?  0.143   14.290  
16  16  24  0.975  0.128       ?  0.143   14.290  
17  17   6  0.980  0.038       ?  0.914  100.000  
18  18   1  0.994  0.071       ?  0.910  100.000  
19  19   1  0.994  0.160       ?  0.775    0.000  
20  20   1  0.978  0.059       ?  0.702    0.000  
21  21   1  0.997  0.145       ?  0.626    0.000  
22  22   1  0.895  0.121       ?  0.826  100.000  
23  23   1  0.618  0.140       ?  0.679    0.000  
24  24   1  0.787  0.160       ?  0.484    0.000  
25  25   1  0.957  0.080       ?  0.581    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        "2022.3.0, CSD as543be (2022)"                                        Y  
3  eds          3.0                                                                   Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.20.1                                                                Y  
6  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
