Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound details
THE LIGAND DENOTED AS PGT HAS BEEN CO-PURIFIED ALONG WITH THE PROTEIN AND ITS EXACT IDENTITY IS NOT ...THE LIGAND DENOTED AS PGT HAS BEEN CO-PURIFIED ALONG WITH THE PROTEIN AND ITS EXACT IDENTITY IS NOT KNOWN. PGT REPRESENTS A CLOSE MATCH
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal grow
Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 18% PEG 4000, 100 mM Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution: 2→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.66 / Num. unique all: 2077 / % possible all: 97.3
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SHELXS
phasing
REFMAC
5.5.0070
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SIRAS / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU B: 12.312 / SU ML: 0.149 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: A PEG4000 FRAGMENT (PGE) FROM CRYSTALLIZATION SOLUTION AND A GLYCEROL MOLECULE (GOL) FROM CRYO SOLUTION ARE MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25182
1095
5 %
RANDOM
Rwork
0.22119
-
-
-
obs
0.22275
20652
99.35 %
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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: 37 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.34 Å2
0 Å2
0 Å2
2-
-
0.95 Å2
0 Å2
3-
-
-
-1.29 Å2
Refinement step
Cycle: LAST / Resolution: 2→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2153
0
110
146
2409
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
2317
X-RAY DIFFRACTION
r_bond_other_d
0.005
0.02
1624
X-RAY DIFFRACTION
r_angle_refined_deg
1.723
2.008
3123
X-RAY DIFFRACTION
r_angle_other_deg
0.916
3.016
3786
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.61
5
278
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.11
24.444
90
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.266
15
375
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.48
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.098
0.2
354
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
2448
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
435
X-RAY DIFFRACTION
r_mcbond_it
0.886
1.5
1387
X-RAY DIFFRACTION
r_mcbond_other
0.225
1.5
562
X-RAY DIFFRACTION
r_mcangle_it
1.679
2
2244
X-RAY DIFFRACTION
r_scbond_it
2.42
3
930
X-RAY DIFFRACTION
r_scangle_it
3.965
4.5
878
Refine LS restraints NCS
Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Dom-ID
Number
Type
Rms dev position (Å)
Weight position
1
1
802
tightpositional
0.04
0.05
2
2
109
mediumpositional
0.43
0.5
1
1
944
loosepositional
0.04
5
1
1
802
tightthermal
0.12
0.5
2
2
109
mediumthermal
0.25
2
1
1
944
loosethermal
0.13
10
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.341
65
-
Rwork
0.29
1444
-
obs
-
-
96.85 %
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
3.1501
-0.381
-0.3873
1.9341
1.197
2.573
0.0765
0.1117
-0.0612
0.0005
-0.1244
0.0079
-0.1019
-0.271
0.0479
0.0159
-0.0171
0.0044
0.5087
0.0155
0.2007
12.378
33.346
21.571
2
3.399
1.7343
-0.3644
3.7946
-0.819
11.9989
-0.0907
0.2865
-0.0746
0.1752
0.2543
-0.3486
-0.7914
0.2686
-0.1636
0.0718
-0.0271
-0.0061
0.4933
-0.023
0.3066
30.519
32.502
25.222
3
4.0954
-0.2251
1.4621
2.6053
0.6348
3.6825
0.0483
0.3628
0.0677
-0.171
-0.0544
-0.1268
-0.3759
-0.062
0.0061
0.0597
-0.0084
0.0371
0.4403
-0.011
0.192
17.63
36.875
22.2
4
10.1323
-2.386
2.0454
5.1584
-0.6746
3.9237
0.1747
0.4116
-0.0282
-0.1919
-0.143
-0.0047
-0.1359
-0.2527
-0.0317
0.0379
-0.0181
0.0536
0.4491
-0.0135
0.1602
13.586
30.194
18.343
5
3.5613
0.4822
-0.8243
1.9737
-1.2113
2.2123
0.1179
-0.2331
-0.0168
0.014
-0.205
0.0345
-0.1262
0.1598
0.087
0.032
0.0189
-0.0075
0.5421
-0.0539
0.178
27.69
32.956
-8.62
6
2.2578
-2.4176
-0.7269
4.5399
1.1069
11.2282
-0.0032
-0.4794
0.1281
-0.1907
0.2623
0.319
-0.8321
0.0652
-0.2591
0.1017
0.0226
-0.0196
0.6364
-0.0271
0.2827
9.466
32.215
-12.281
7
3.9364
1.3409
0.345
1.8489
-0.3959
3.3656
0.3105
-0.4187
0.1517
0.2349
-0.1507
0.1172
-0.4119
0.0796
-0.1598
0.1016
0.0311
0.0159
0.4802
-0.0223
0.2211
22.358
36.635
-9.303
8
9.8664
2.6521
2.0466
5.4168
1.7071
5.0445
0.3015
-0.4998
0.0323
0.1992
-0.3271
0.0843
0.0057
0.1421
0.0256
0.0464
0.0198
0.0311
0.5248
-0.0485
0.1358
26.317
29.844
-5.363
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
21 - 93
2
X-RAY DIFFRACTION
2
A
94 - 110
3
X-RAY DIFFRACTION
3
A
111 - 132
4
X-RAY DIFFRACTION
4
A
133 - 158
5
X-RAY DIFFRACTION
5
B
19 - 93
6
X-RAY DIFFRACTION
6
B
94 - 110
7
X-RAY DIFFRACTION
7
B
111 - 132
8
X-RAY DIFFRACTION
8
B
133 - 158
+
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