data_7TME

_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  7TME
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7TME
_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        2024-09-17:14:14
_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  ACETONITRILE  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  2  
D  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  0.8  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   35.05  180529     ?     ?  
 2  2  1   27.39    1424  0.60  1.00  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1340  0.60  1.00  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1341  0.60  1.00  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1276  0.60  1.00  
 9  1  5   99.71  164625     ?     ?  
10  2  5   78.04    1279  0.60  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      0.69
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.33
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   74
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  95
#
_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                     7.33
_pdbx_vrpt_summary_geometry.num_H_reduce                   99
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 74
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.33
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                95
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.69
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            57.162
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         4.807
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.10(0.74A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        12125
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.356
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.508
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.343
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.972
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1138
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1312
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1166
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.80
_pdbx_vrpt_summary_diffraction.EDS_res_low               12.14
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[6.315,4.589,3.692,0.000,-0.067,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.539
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 29.23 % 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 1.6075e-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         4
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         96.51
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      9538
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.04
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       0.80
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        12.14
_pdbx_vrpt_summary_diffraction.PDB_R                     0.11
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.12
_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  ?        1     ?  
 2  1  1  A   1  I6W  A    1  B  ?        2     ?  
 3  1  1  A   2  LEU  A    2  A  ?        ?     ?  
 4  1  1  A   2  LEU  A    2  B  ?        ?     ?  
 5  1  1  A   3  AIB  A    3  .  ?        ?     ?  
 6  1  1  A   4  ALA  A    4  .  ?        ?     ?  
 7  1  1  A   5  ASP  A    5  A  ?        ?     ?  
 8  1  1  A   5  ASP  A    5  B  ?        ?     ?  
 9  1  1  A   6  LEU  A    6  A  ?        ?     ?  
10  1  1  A   6  LEU  A    6  B  ?        ?     ?  
11  1  1  A   7  AIB  A    7  .  ?        ?     2  
12  1  1  A   8  GLN  A    8  .  ?        ?     ?  
13  1  1  A   9  AIB  A    9  .  ?        ?     ?  
14  1  1  A  10  LEU  A   10  A  ?        ?     ?  
15  1  1  A  10  LEU  A   10  B  ?        ?     ?  
16  1  1  A  11  I77  A   11  A  ?        ?     ?  
17  1  1  A  11  I77  A   11  B  ?        ?     ?  
18  1  2  B   .  CCN  A  201  .  ?        ?     ?  
19  1  2  C   .  CCN  A  202  .  ?        ?     ?  
20  1  3  D   .  HOH  A  301  .  ?        1     ?  
21  1  3  D   .  HOH  A  302  .  ?        ?     ?  
22  1  3  D   .  HOH  A  303  .  ?        ?     ?  
23  1  3  D   .  HOH  A  304  .  ?        ?     ?  
24  1  3  D   .  HOH  A  305  .  ?        ?     ?  
25  1  3  D   .  HOH  A  306  .  ?        ?     ?  
26  1  3  D   .  HOH  A  307  .  ?        ?     ?  
27  1  3  D   .  HOH  A  308  .  ?        ?     ?  
28  1  3  D   .  HOH  A  309  .  ?        ?     ?  
29  1  3  D   .  HOH  A  310  .  ?        ?     ?  
30  1  3  D   .  HOH  A  311  .  ?        ?     ?  
31  1  3  D   .  HOH  A  312  .  ?        ?     ?  
32  1  3  D   .  HOH  A  313  .  ?        ?     ?  
33  1  3  D   .  HOH  A  314  .  ?        ?     ?  
34  1  3  D   .  HOH  A  315  .  ?        ?     ?  
35  1  3  D   .  HOH  A  316  .  ?        ?     ?  
#
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  ?         ?      ?  ?           ?   4.970     ?     ?     ?     ?  ?           0.500  
 2   2  ?         ?      ?  ?           ?   4.970     ?     ?     ?     ?  ?           0.500  
 3   3  tp        ?      ?  ?          10   3.100     7  0.20     8  0.18  molprobity  0.500  
 4   4  tp        ?      ?  ?          10   3.100     7  0.20     8  0.18  molprobity  0.500  
 5   5  ?         ?      ?  ?           6   5.530     1  1.09     0     ?  mogul       1.000  
 6   6  ?     -60.1  -36.5  Favored     5   6.290     5  0.24     7  0.57  molprobity  1.000  
 7   7  m-20  -74.2  -12.5  Favored     4   2.820     8  0.46    11  1.19  molprobity  0.500  
 8   8  m-20  -74.2  -12.5  Favored     4   2.820     8  0.46    11  1.19  molprobity  0.500  
 9   9  mt    -95.5  -46.2  Favored     ?   6.010     7  0.39     8  0.27  molprobity  1.000  
10  10  mt    -95.5  -46.2  Favored     ?   6.010     7  0.39     8  0.27  molprobity  1.000  
11  11  ?         ?      ?  ?           7   5.620     1  1.16     0     ?  mogul       1.000  
12  12  pt20  -55.3  -26.9  Favored     8   4.060     8  0.25     9  0.30  molprobity  1.000  
13  13  ?         ?      ?  ?           7   4.360     1  1.16     0     ?  mogul       1.000  
14  14  mt        ?      ?  ?          11   2.540     7  0.27     8  0.65  molprobity  0.500  
15  15  mt        ?      ?  ?          11   2.540     7  0.27     8  0.65  molprobity  0.500  
16  16  ?         ?      ?  ?           ?   2.630     ?     ?     ?     ?  ?           0.500  
17  17  ?         ?      ?  ?           ?   2.630     ?     ?     ?     ?  ?           0.500  
18  18  ?         ?      ?  ?           3  10.410     2  0.87     1  0.50  mogul       1.000  
19  19  ?         ?      ?  ?           3   6.380     2  0.71     1  0.58  mogul       1.000  
20  20  ?         ?      ?  ?           ?  30.020     ?     ?     ?     ?  ?           1.000  
21  21  ?         ?      ?  ?           ?  19.680     ?     ?     ?     ?  ?           1.000  
22  22  ?         ?      ?  ?           ?   9.420     ?     ?     ?     ?  ?           1.000  
23  23  ?         ?      ?  ?           ?  41.110     ?     ?     ?     ?  ?           1.000  
24  24  ?         ?      ?  ?           ?  21.060     ?     ?     ?     ?  ?           1.000  
25  25  ?         ?      ?  ?           ?  31.190     ?     ?     ?     ?  ?           1.000  
26  26  ?         ?      ?  ?           ?  23.460     ?     ?     ?     ?  ?           1.000  
27  27  ?         ?      ?  ?           ?  39.680     ?     ?     ?     ?  ?           1.000  
28  28  ?         ?      ?  ?           ?  29.610     ?     ?     ?     ?  ?           1.000  
29  29  ?         ?      ?  ?           ?  41.930     ?     ?     ?     ?  ?           1.000  
30  30  ?         ?      ?  ?           ?  31.710     ?     ?     ?     ?  ?           1.000  
31  31  ?         ?      ?  ?           ?  37.020     ?     ?     ?     ?  ?           1.000  
32  32  ?         ?      ?  ?           ?  33.810     ?     ?     ?     ?  ?           1.000  
33  33  ?         ?      ?  ?           ?  38.270     ?     ?     ?     ?  ?           1.000  
34  34  ?         ?      ?  ?           ?  45.440     ?     ?     ?     ?  ?           1.000  
35  35  ?         ?      ?  ?           ?  34.820     ?     ?     ?     ?  ?           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   1  O17  1  0.77  2.02  
2   2  O17  2  0.54  2.54  
3   2  C16  2  0.54  2.54  
4  20  O    1  0.77  2.02  
#
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  11  O  C  CA  CB1   35.08  53.98  50  29.53  3.80  2.00  
2  11  O  C  CA  CB2  -81.78  46.12  50  22.87  5.76  4.00  
#
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  60  0.889  0.170       ?  0.331    2.710  
 2   2  60  0.889  0.170       ?  0.331    2.710  
 3   3  36  0.964  0.064   0.485  0.723   33.820  
 4   4  36  0.964  0.064   0.485  0.723   33.820  
 5   5  13  0.996  0.035       ?  0.873   83.330  
 6   6  10  0.994  0.029  -0.745  0.866   80.000  
 7   7  24  0.985  0.044  -0.509  0.744   46.240  
 8   8  24  0.985  0.044  -0.509  0.744   46.240  
 9   9  20  0.994  0.027  -1.089  0.902  100.000  
10  10  20  0.994  0.027  -1.089  0.902  100.000  
11  11  13  0.995  0.038       ?  0.881   83.330  
12  12  17  0.996  0.027  -0.995  0.840   55.560  
13  13  13  0.996  0.021       ?  0.823   66.670  
14  14  38  0.990  0.042  -0.451  0.769   64.830  
15  15  38  0.990  0.042  -0.451  0.769   64.830  
16  16  56  0.981  0.054       ?  0.603    4.660  
17  17  56  0.981  0.054       ?  0.603    4.660  
18  18   6  0.942  0.079       ?  0.845   66.670  
19  19   6  0.989  0.033       ?  0.963  100.000  
20  20   1  0.679  0.313       ?  0.401    0.000  
21  21   1  0.940  0.098       ?  0.947  100.000  
22  22   1  0.985  0.086       ?  0.983  100.000  
23  23   1  0.708  0.180       ?  0.324    0.000  
24  24   1  0.905  0.145       ?  0.818  100.000  
25  25   1  0.838  0.113       ?  0.529    0.000  
26  26   1  0.930  0.083       ?  0.778    0.000  
27  27   1  0.794  0.155       ?  0.357    0.000  
28  28   1  0.764  0.146       ?  0.893  100.000  
29  29   1  0.853  0.213       ?  0.474    0.000  
30  30   1  0.830  0.095       ?  0.509    0.000  
31  31   1  0.836  0.135       ?  0.472    0.000  
32  32   1  0.919  0.102       ?  0.589    0.000  
33  33   1  0.840  0.108       ?  0.389    0.000  
34  34   1  0.762  0.109       ?  0.109    0.000  
35  35   1  0.727  0.115       ?  0.233    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  
##
