data_1Z7I

loop_
_pdbx_vrpt_database.id
_pdbx_vrpt_database.code
PDB  1Z7I    
NDB  AD0045  
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1Z7I
_pdbx_vrpt_summary.PDB_deposition_date         2005-03-24
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-02-14
_pdbx_vrpt_summary.report_creation_date        2024-02-06:00:48
_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      "5'-D(*GP*(UMS)P*GP*TP*AP*CP*AP*C)-3'"  
2  non-polymer  SPERMINE  
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  1.28  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore    
2  RSRZ_outliers_percent  
3  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   66.84  141614     ?     ?  
2  2  1   51.19    1926  1.26  1.30  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1807  1.26  1.30  
5  1  3   84.49  130704     ?     ?  
6  2  3   26.33    1850  1.26  1.30  
#
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  
#
_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      1.47
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       1.50
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   158
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  242
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       3.86
_pdbx_vrpt_summary_geometry.num_H_reduce     94
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   158
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.50
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  242
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.47
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 65.704
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            36.746
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         12.421
_pdbx_vrpt_summary_diffraction.I_over_sigma              2.84(1.25A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        6301
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.225
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.335
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.482
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.317
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.969
_pdbx_vrpt_summary_diffraction.DCC_R                     0.18
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.20
_pdbx_vrpt_summary_diffraction.EDS_R                     0.18
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.25
_pdbx_vrpt_summary_diffraction.EDS_res_low               20.80
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[12.988,12.988,11.383,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.129
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 15.40% 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         95.41
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      690
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.95
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.28
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        20.81
_pdbx_vrpt_summary_diffraction.PDB_R                     0.18
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.20
#
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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.count_plane_outliers
_pdbx_vrpt_model_instance.count_mogul_bond_outliers
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
 1  1  1  A  1  DG   A   1  .  ?        1     ?     ?     ?     ?  
 2  1  1  A  2  UMS  A   2  .  ?        ?     ?     ?     1     2  
 3  1  1  A  3  DG   A   3  .  ?        1     ?     ?     ?     ?  
 4  1  1  A  4  DT   A   4  .  ?        1     ?     ?     ?     ?  
 5  1  1  A  5  DA   A   5  .  ?        ?     ?     ?     ?     ?  
 6  1  1  A  6  DC   A   6  .  ?        ?     ?     ?     ?     ?  
 7  1  1  A  7  DA   A   7  .  ?        ?     1     ?     ?     ?  
 8  1  1  A  8  DC   A   8  .  ?        ?     ?     1     ?     ?  
 9  1  2  B  .  SPM  A  50  .  ?        ?     1     ?     ?     ?  
10  1  3  C  .  HOH  A  51  .  ?        ?     ?     ?     ?     ?  
11  1  3  C  .  HOH  A  52  .  ?        ?     ?     ?     ?     ?  
12  1  3  C  .  HOH  A  53  .  ?        ?     ?     ?     ?     ?  
13  1  3  C  .  HOH  A  54  .  ?        ?     ?     ?     ?     ?  
14  1  3  C  .  HOH  A  55  .  ?        ?     ?     ?     ?     ?  
15  1  3  C  .  HOH  A  56  .  ?        ?     ?     ?     ?     ?  
16  1  3  C  .  HOH  A  57  .  ?        ?     ?     ?     ?     ?  
17  1  3  C  .  HOH  A  58  .  ?        ?     ?     ?     ?     ?  
18  1  3  C  .  HOH  A  59  .  ?        ?     ?     ?     ?     ?  
19  1  3  C  .  HOH  A  60  .  ?        ?     ?     ?     ?     ?  
20  1  3  C  .  HOH  A  61  .  ?        ?     ?     ?     ?     ?  
21  1  3  C  .  HOH  A  62  .  ?        ?     ?     ?     ?     ?  
22  1  3  C  .  HOH  A  63  .  ?        ?     ?     ?     ?     ?  
23  1  3  C  .  HOH  A  64  .  ?        ?     ?     ?     ?     ?  
24  1  3  C  .  HOH  A  65  .  ?        ?     ?     ?     ?     ?  
25  1  3  C  .  HOH  A  66  .  ?        ?     ?     ?     ?     ?  
26  1  3  C  .  HOH  A  67  .  ?        ?     ?     ?     ?     ?  
27  1  3  C  .  HOH  A  68  .  ?        ?     ?     ?     ?     ?  
28  1  3  C  .  HOH  A  69  .  ?        ?     ?     ?     ?     ?  
29  1  3  C  .  HOH  A  70  .  ?        ?     ?     ?     ?     ?  
30  1  3  C  .  HOH  A  71  .  ?        ?     ?     ?     ?     ?  
31  1  3  C  .  HOH  A  72  .  ?        ?     ?     ?     ?     ?  
32  1  3  C  .  HOH  A  73  .  ?        ?     ?     ?     ?     ?  
33  1  3  C  .  HOH  A  74  .  ?        ?     ?     ?     ?     ?  
34  1  3  C  .  HOH  A  75  .  ?        ?     ?     ?     ?     ?  
35  1  3  C  .  HOH  A  76  .  ?        ?     ?     ?     ?     ?  
36  1  3  C  .  HOH  A  77  .  ?        ?     ?     ?     ?     ?  
37  1  3  C  .  HOH  A  78  .  ?        ?     ?     ?     ?     ?  
38  1  3  C  .  HOH  A  79  .  ?        ?     ?     ?     ?     ?  
39  1  3  C  .  HOH  A  80  .  ?        ?     ?     ?     ?     ?  
40  1  3  C  .  HOH  A  81  .  ?        ?     ?     ?     ?     ?  
41  1  3  C  .  HOH  A  82  .  ?        ?     ?     ?     ?     ?  
42  1  3  C  .  HOH  A  83  .  ?        ?     ?     ?     ?     ?  
43  1  3  C  .  HOH  A  84  .  ?        ?     ?     ?     ?     ?  
44  1  3  C  .  HOH  A  85  .  ?        ?     ?     ?     ?     ?  
45  1  3  C  .  HOH  A  86  .  ?        ?     ?     ?     ?     ?  
46  1  3  C  .  HOH  A  87  .  ?        ?     ?     ?     ?     ?  
47  1  3  C  .  HOH  A  88  .  ?        ?     ?     ?     ?     ?  
48  1  3  C  .  HOH  A  89  .  ?        ?     ?     ?     ?     ?  
49  1  3  C  .  HOH  A  90  .  ?        ?     ?     ?     ?     ?  
50  1  3  C  .  HOH  A  91  .  ?        ?     ?     ?     ?     ?  
51  1  3  C  .  HOH  A  92  .  ?        ?     ?     ?     ?     ?  
52  1  3  C  .  HOH  A  93  .  ?        ?     ?     ?     ?     ?  
53  1  3  C  .  HOH  A  94  .  ?        ?     ?     ?     ?     ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_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    12  11.430    21  1.36    31  1.82  molprobity  1.000  
 2   2    12  12.300    17  1.06    24  1.12  mogul       1.000  
 3   3    11  12.470    25  1.74    39  2.09  molprobity  1.000  
 4   4    12  11.750    22  1.67    34  1.89  molprobity  1.000  
 5   5    11  10.180    24  1.26    37  0.87  molprobity  1.000  
 6   6    11  10.720    21  1.40    32  0.94  molprobity  1.000  
 7   7    11  11.150    24  1.54    37  0.93  molprobity  1.000  
 8   8    12  14.430    20  1.39    28  0.82  molprobity  1.000  
 9   9     2  22.910     2  1.35     0     ?  mogul       1.000  
10  10     ?   9.760     ?     ?     ?     ?  ?           1.000  
11  11     ?  16.570     ?     ?     ?     ?  ?           1.000  
12  12     ?  15.370     ?     ?     ?     ?  ?           1.000  
13  13     ?  17.020     ?     ?     ?     ?  ?           1.000  
14  14     ?  19.730     ?     ?     ?     ?  ?           1.000  
15  15     ?  19.140     ?     ?     ?     ?  ?           1.000  
16  16     ?  18.190     ?     ?     ?     ?  ?           1.000  
17  17     ?  16.290     ?     ?     ?     ?  ?           1.000  
18  18     ?  17.630     ?     ?     ?     ?  ?           1.000  
19  19     ?  20.970     ?     ?     ?     ?  ?           1.000  
20  20     ?  18.450     ?     ?     ?     ?  ?           1.000  
21  21     ?  18.600     ?     ?     ?     ?  ?           1.000  
22  22     ?  20.910     ?     ?     ?     ?  ?           1.000  
23  23     ?  22.420     ?     ?     ?     ?  ?           1.000  
24  24     ?  22.500     ?     ?     ?     ?  ?           1.000  
25  25     ?  20.430     ?     ?     ?     ?  ?           1.000  
26  26     ?  22.740     ?     ?     ?     ?  ?           1.000  
27  27     ?  23.050     ?     ?     ?     ?  ?           1.000  
28  28     ?  28.840     ?     ?     ?     ?  ?           1.000  
29  29     ?  26.670     ?     ?     ?     ?  ?           1.000  
30  30     ?  24.970     ?     ?     ?     ?  ?           1.000  
31  31     ?  30.660     ?     ?     ?     ?  ?           1.000  
32  32     ?  26.490     ?     ?     ?     ?  ?           1.000  
33  33     ?  31.280     ?     ?     ?     ?  ?           1.000  
34  34     ?  27.420     ?     ?     ?     ?  ?           1.000  
35  35     ?  25.020     ?     ?     ?     ?  ?           1.000  
36  36     ?  33.720     ?     ?     ?     ?  ?           1.000  
37  37     ?  27.430     ?     ?     ?     ?  ?           1.000  
38  38     ?  35.370     ?     ?     ?     ?  ?           1.000  
39  39     ?  32.870     ?     ?     ?     ?  ?           1.000  
40  40     ?  32.040     ?     ?     ?     ?  ?           1.000  
41  41     ?  25.920     ?     ?     ?     ?  ?           0.500  
42  42     ?  31.160     ?     ?     ?     ?  ?           1.000  
43  43     ?  34.400     ?     ?     ?     ?  ?           1.000  
44  44     ?  32.130     ?     ?     ?     ?  ?           1.000  
45  45     ?  36.800     ?     ?     ?     ?  ?           1.000  
46  46     ?  32.270     ?     ?     ?     ?  ?           1.000  
47  47     ?  32.680     ?     ?     ?     ?  ?           1.000  
48  48     ?  31.030     ?     ?     ?     ?  ?           1.000  
49  49     ?  39.100     ?     ?     ?     ?  ?           1.000  
50  50     ?  35.930     ?     ?     ?     ?  ?           1.000  
51  51     ?  28.240     ?     ?     ?     ?  ?           1.000  
52  52     ?  36.490     ?     ?     ?     ?  ?           1.000  
53  53     ?  37.620     ?     ?     ?     ?  ?           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  7  N7  1  0.46  2.79  
2  9  C6  1  0.46  2.79  
#
_pdbx_vrpt_instance_intra_plane_outliers.ordinal      1
_pdbx_vrpt_instance_intra_plane_outliers.instance_id  8
_pdbx_vrpt_instance_intra_plane_outliers.type         sidechain
_pdbx_vrpt_instance_intra_plane_outliers.plane_rmsd   0.07
#
loop_
_pdbx_vrpt_instance_intra_angle_outliers.ordinal
_pdbx_vrpt_instance_intra_angle_outliers.instance_id
_pdbx_vrpt_instance_intra_angle_outliers.atom_1
_pdbx_vrpt_instance_intra_angle_outliers.atom_2
_pdbx_vrpt_instance_intra_angle_outliers.atom_3
_pdbx_vrpt_instance_intra_angle_outliers.obs
_pdbx_vrpt_instance_intra_angle_outliers.mean
_pdbx_vrpt_instance_intra_angle_outliers.stdev
_pdbx_vrpt_instance_intra_angle_outliers.Z
1  1  "O4'"  "C1'"  N9  101.879  108.000  0.700  -8.74  
2  3  "O4'"  "C1'"  N9  102.268  108.000  0.700  -8.19  
3  4  "O4'"  "C1'"  N1  102.019  108.000  0.700  -8.54  
#
_pdbx_vrpt_instance_mogul_bond_outliers.ordinal      1
_pdbx_vrpt_instance_mogul_bond_outliers.instance_id  2
_pdbx_vrpt_instance_mogul_bond_outliers.atom_1       "O3'"
_pdbx_vrpt_instance_mogul_bond_outliers.atom_2       "C3'"
_pdbx_vrpt_instance_mogul_bond_outliers.obsval       1.35
_pdbx_vrpt_instance_mogul_bond_outliers.mean         1.43
_pdbx_vrpt_instance_mogul_bond_outliers.numobs       10000
_pdbx_vrpt_instance_mogul_bond_outliers.stdev        0.02
_pdbx_vrpt_instance_mogul_bond_outliers.Zscore       -3.02
_pdbx_vrpt_instance_mogul_bond_outliers.mindiff      0.00
#
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  2  "O4'"  "C1'"  N1  103.17  108.36  1007  2.29  -2.27  0.05  
2  2  "C2'"  "C1'"  N1  104.82  113.99    23  3.39  -2.70  2.06  
#
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  19  0.966  0.063  -0.577  
 2   2  21  0.988  0.059       ?  
 3   3  22  0.932  0.091   0.402  
 4   4  20  0.965  0.074   0.023  
 5   5  21  0.971  0.068  -0.200  
 6   6  19  0.978  0.061  -0.617  
 7   7  21  0.962  0.074  -0.036  
 8   8  19  0.966  0.078  -0.120  
 9   9   3  0.780  0.220       ?  
10  10   1  0.996  0.028       ?  
11  11   1  0.984  0.068       ?  
12  12   1  0.978  0.063       ?  
13  13   1  0.963  0.069       ?  
14  14   1  0.976  0.065       ?  
15  15   1  0.969  0.067       ?  
16  16   1  0.979  0.070       ?  
17  17   1  0.974  0.085       ?  
18  18   1  0.974  0.065       ?  
19  19   1  0.940  0.140       ?  
20  20   1  0.952  0.079       ?  
21  21   1  0.907  0.099       ?  
22  22   1  0.941  0.082       ?  
23  23   1  0.937  0.109       ?  
24  24   1  0.920  0.144       ?  
25  25   1  0.969  0.102       ?  
26  26   1  0.959  0.100       ?  
27  27   1  0.955  0.164       ?  
28  28   1  0.915  0.094       ?  
29  29   1  0.870  0.153       ?  
30  30   1  0.919  0.193       ?  
31  31   1  0.940  0.112       ?  
32  32   1  0.953  0.253       ?  
33  33   1  0.774  0.143       ?  
34  34   1  0.872  0.207       ?  
35  35   1  0.935  0.096       ?  
36  36   1  0.851  0.136       ?  
37  37   1  0.597  0.321       ?  
38  38   1  0.792  0.146       ?  
39  39   1  0.823  0.135       ?  
40  40   1  0.799  0.169       ?  
41  41   1  0.921  0.446       ?  
42  42   1  0.891  0.108       ?  
43  43   1  0.637  0.198       ?  
44  44   1  0.863  0.389       ?  
45  45   1  0.758  0.238       ?  
46  46   1  0.846  0.168       ?  
47  47   1  0.824  0.276       ?  
48  48   1  0.860  0.221       ?  
49  49   1  0.685  0.126       ?  
50  50   1  0.868  0.137       ?  
51  51   1  0.882  0.162       ?  
52  52   1  0.358  0.227       ?  
53  53   1  0.771  0.251       ?  
#
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        "1.8.5 (274361), 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  
##
