Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta Similarity search - Domain/homology
Resolution: 1.75→37.92 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 7.129 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28104
1168
5.1 %
RANDOM
Rwork
0.22126
-
-
-
obs
0.22434
21540
94.72 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 16.296 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.03 Å2
0 Å2
0 Å2
2-
-
0.02 Å2
-0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.75→37.92 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1687
0
1
103
1791
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.021
1737
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1182
X-RAY DIFFRACTION
r_angle_refined_deg
1.999
1.967
2340
X-RAY DIFFRACTION
r_angle_other_deg
2.263
3
2866
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.429
5
212
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.134
24.198
81
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.053
15
278
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.749
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.138
0.2
238
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
1948
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
357
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.948
1.5
1059
X-RAY DIFFRACTION
r_mcbond_other
0.349
1.5
435
X-RAY DIFFRACTION
r_mcangle_it
1.394
2
1690
X-RAY DIFFRACTION
r_scbond_it
2.458
3
678
X-RAY DIFFRACTION
r_scangle_it
3.613
4.5
649
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.75→1.795 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.327
95
-
Rwork
0.265
1618
-
obs
-
-
99.71 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
4.7957
1.9052
-0.6878
12.7509
0.5822
-0.6803
-0.1792
-0.2377
-0.3637
0.3574
0.2755
-0.5147
0.0222
0.0764
-0.0963
0.0584
0.0113
-0.0563
0.1326
0.0004
0.0863
25.2083
11.9086
29.3144
2
0.6787
0.7783
1.2316
1.6586
1.0507
3.5781
-0.0934
0.1652
-0.0241
-0.2632
0.1076
-0.1347
0.0912
0.1422
-0.0142
0.1129
0.0204
0.0098
0.1181
-0.0021
0.0713
23.1543
11.5016
6.4654
3
-0.0651
0.3801
-0.5149
1.4125
2.4763
14.1935
-0.0594
0.0538
-0.0096
-0.272
0.0895
-0.39
-0.0132
0.1297
-0.0301
0.1123
0.0073
0.0115
0.0995
0.0031
0.1019
25.1139
15.3049
8.3424
4
3.6158
0.9875
-0.1771
4.8955
-4.4689
5.9705
-0.1134
-0.1447
0.0028
0.1776
0.1716
0.0524
-0.0716
-0.0785
-0.0582
0.0417
0.0236
-0.0279
0.0775
-0.0039
0.0703
17.5981
14.61
27.5423
5
1.8184
0.3507
-1.249
2.6589
-0.3943
3.5427
-0.0676
0.1642
0.1142
-0.3749
0.0503
-0.0219
-0.1133
0.1279
0.0174
0.0648
-0.0094
-0.017
0.091
0.0316
0.0661
22.8902
19.1547
7.677
6
0.6539
-0.0955
0.6429
3.2842
-2.3784
4.3209
-0.0539
0.135
0.0541
-0.2955
-0.0316
0.05
0.1428
0.1319
0.0856
0.0288
-0.0154
-0.0213
0.1265
0.0058
0.0814
14.7375
13.3229
7.5713
7
3.0428
0.0678
-1.4718
0.2291
0.4189
0.8376
0.0023
-0.1395
0.09
0.1727
0.0224
0.1391
-0.0237
0.0301
-0.0247
0.0726
0.0048
0.007
0.1159
0.019
0.0734
13.1922
4.5789
27.7255
8
1.5532
0.2625
0.7526
1.1714
-0.5718
1.7221
0.0922
0.1098
-0.0446
-0.1399
-0.06
-0.1812
0.107
0.147
-0.0322
0.0347
0.0111
0
0.0984
-0.0082
0.0805
19.5583
0.647
17.071
9
4.3558
0.7057
-1.309
3.7054
-0.4819
2.9821
-0.2084
0.1688
-0.3688
-0.3073
0.1566
0.2402
0.0684
-0.2819
0.0518
0.1597
0.0026
-0.0471
0.161
0.0048
0.0662
5.0073
7.1037
0.2482
10
4.8693
3.8919
5.1272
3.7011
3.1903
8.2477
0.1112
0.2013
-0.2698
-0.0594
0.1165
-0.3424
-0.0478
0.3456
-0.2277
0.1068
0.0222
0.0132
0.0698
-0.0127
0.0987
23.5184
3.3121
13.1833
11
3.0463
0.3084
3.0942
1.3241
0.0452
5.066
-0.0138
0.2093
-0.1202
-0.1622
0.1224
-0.2224
0.0831
0.1779
-0.1086
0.0388
0.0071
0.0377
0.0842
0.0091
0.0802
22.9434
7.1717
10.389
12
1.5818
1.5704
-0.0878
16.0938
9.4227
7.0628
-0.0991
0.3312
0.1976
-0.3747
0.126
0.2601
-0.1621
-0.1075
-0.027
0.1847
-0.0344
-0.0784
0.1789
0.0599
0.0332
7.1068
16.4489
-5.2803
13
6.4134
0.7
-1.2348
-2.106
-0.4424
12.2472
-0.0475
-0.0588
-0.1583
0.0962
-0.0023
0.0832
-0.1641
-0.3184
0.0499
0.0446
0.0244
-0.0451
0.0902
0.0239
0.1156
4.6476
17.2157
10.1721
14
1.9637
-4.0956
1.1351
8.7232
-3.3841
2.1456
0.0356
-0.011
-0.2825
-0.3783
0.1966
0.7152
0.0861
-0.1046
-0.2322
0.0177
-0.0085
-0.0522
0.1333
0.0076
0.164
6.2433
-2.4339
17.6992
15
1.6205
1.6554
-0.8859
5.8698
1.0217
0.4918
0.1386
0.1306
0.2719
-0.1423
-0.1509
0.4674
-0.036
-0.1091
0.0123
0.0909
0.0168
-0.0552
0.177
0.0394
0.1231
1.186
14.8813
6.0082
16
13.3149
4.3957
5.7197
0.5904
-0.5103
6.9201
0.1386
-0.1842
-0.7698
0.0879
0.2746
0.1832
0.1865
-0.4605
-0.4132
0.076
0.0024
-0.0107
0.0956
0.0221
0.1292
11.7689
-1.5099
13.6568
17
0.6606
-1.5788
-0.5414
2.1604
0.0263
0.1756
0.0514
-0.0592
0.0741
0.0107
0.0253
0.0643
0.0367
0.0063
-0.0767
0.0466
-0.0089
-0.0255
0.105
-0.0041
0.0772
12.6514
-2.7214
23.8987
18
8.922
9.2813
-7.228
14.7175
-9.7708
7.065
0.0215
-0.0186
0.1657
-0.2317
-0.0381
0.1306
0.1584
-0.0324
0.0166
0.0797
0.003
-0.028
0.109
0.0077
0.0824
9.1931
17.4387
15.9156
19
8.3574
14.1549
1.2016
18.8973
11.3019
11.5726
-0.0066
0.1034
0.8578
-1.0943
0.7364
0.7898
-1.0141
1.0632
-0.7298
0.2373
-0.0295
0.0069
0.1812
0.0583
0.1989
17.9688
25.7294
3.5425
20
5.4248
5.5407
-4.6839
8.2379
-5.3243
3.9476
0.1348
-0.1079
-0.0085
0.1466
-0.1324
0.2347
-0.1677
0.0526
-0.0024
0.0583
-0.0164
-0.0348
0.127
0.0188
0.0639
10.3589
14.6032
20.4343
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
6 - 11
2
X-RAY DIFFRACTION
2
A
12 - 26
3
X-RAY DIFFRACTION
3
A
27 - 34
4
X-RAY DIFFRACTION
4
A
35 - 41
5
X-RAY DIFFRACTION
5
A
42 - 53
6
X-RAY DIFFRACTION
6
A
54 - 71
7
X-RAY DIFFRACTION
7
A
72 - 84
8
X-RAY DIFFRACTION
8
A
85 - 96
9
X-RAY DIFFRACTION
9
A
97 - 105
10
X-RAY DIFFRACTION
10
A
106 - 114
11
X-RAY DIFFRACTION
11
A
115 - 128
12
X-RAY DIFFRACTION
12
A
129 - 140
13
X-RAY DIFFRACTION
13
A
141 - 146
14
X-RAY DIFFRACTION
14
A
147 - 160
15
X-RAY DIFFRACTION
15
A
161 - 177
16
X-RAY DIFFRACTION
16
A
178 - 182
17
X-RAY DIFFRACTION
17
A
183 - 195
18
X-RAY DIFFRACTION
18
A
196 - 202
19
X-RAY DIFFRACTION
19
A
203 - 209
20
X-RAY DIFFRACTION
20
A
210 - 222
+
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