Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. DNA SEQUENCING REVEALED THAT RESIDUE 272 WAS GLY AND RESIDUE 311 WAS HIS IN THE CLONED CONSTRUCT.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.3 Å3/Da / Density % sol: 62.75 %
Resolution: 2→34.816 Å / Num. obs: 91976 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 25.207 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 4.1
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2-2.05
11.1
1.008
0.8
74790
6720
1.008
100
2.05-2.11
11.1
0.819
0.9
72490
6523
0.819
100
2.11-2.17
11.1
0.664
1.2
70418
6325
0.664
100
2.17-2.24
11.1
0.558
1.4
68998
6203
0.558
100
2.24-2.31
11.1
0.458
1.6
66390
5984
0.458
100
2.31-2.39
11.1
0.373
2
64581
5802
0.373
100
2.39-2.48
11.1
0.337
2.2
62346
5603
0.337
100
2.48-2.58
11.1
0.288
2.6
60043
5417
0.288
100
2.58-2.7
11.1
0.237
2.9
57527
5189
0.237
100
2.7-2.83
11
0.196
3.8
55248
5000
0.196
100
2.83-2.98
11
0.154
4.7
52250
4729
0.154
100
2.98-3.16
11
0.125
5.7
49841
4512
0.125
100
3.16-3.38
11
0.106
6.3
46709
4239
0.106
100
3.38-3.65
10.9
0.1
6.2
43319
3974
0.1
100
3.65-4
10.8
0.088
7.1
39537
3656
0.088
100
4-4.47
10.9
0.073
7.8
36446
3359
0.073
100
4.47-5.16
10.8
0.071
8.2
31989
2960
0.071
100
5.16-6.32
10.6
0.073
8.2
27172
2557
0.073
100
6.32-8.94
10.3
0.061
9.2
20859
2028
0.061
100
8.94-34.816
9.4
0.059
9
11193
1196
0.059
98.3
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0067
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2→34.816 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.346 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.115 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE, GLYCEROL, PARTIAL PEG 300 AND IMIDAZOLE FROM CRYSTALLIZATION CONDITION ARE MODELED IN THIS STRUCTURE. 5. UNKNOWN Y-SHAPE ELECTRON DENSITY IS OBSERVED NEAR RESIDUE 18 AND RESIDUE 112 IN SUBUNIT B.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19
4602
5 %
RANDOM
Rwork
0.162
-
-
-
obs
0.164
91891
99.97 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 22.091 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.93 Å2
0.47 Å2
0 Å2
2-
-
0.93 Å2
0 Å2
3-
-
-
-1.4 Å2
Refinement step
Cycle: LAST / Resolution: 2→34.816 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6735
0
192
691
7618
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
7254
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
4955
X-RAY DIFFRACTION
r_angle_refined_deg
1.548
1.954
9820
X-RAY DIFFRACTION
r_angle_other_deg
1.034
3
12012
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.516
5
876
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.333
23.958
331
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.203
15
1131
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.937
15
40
X-RAY DIFFRACTION
r_chiral_restr
0.094
0.2
1009
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
8019
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1495
X-RAY DIFFRACTION
r_mcbond_it
0.802
1.5
4335
X-RAY DIFFRACTION
r_mcbond_other
0.216
1.5
1752
X-RAY DIFFRACTION
r_mcangle_it
1.453
2
6982
X-RAY DIFFRACTION
r_scbond_it
2.421
3
2919
X-RAY DIFFRACTION
r_scangle_it
3.775
4.5
2838
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.275
353
-
Rwork
0.226
6365
-
all
-
6718
-
obs
-
-
100 %
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
0.8978
-0.3131
0.6455
0.3013
0.2139
1.5428
-0.0302
0.0994
0.0545
-0.1016
0.0767
-0.0384
-0.0989
0.2909
-0.0466
-0.0533
-0.0499
-0.0003
0.0406
-0.0195
-0.0637
87.7843
17.7828
21.8871
2
0.6344
-0.0834
-0.1927
0.6083
0.1812
1.3274
-0.0529
0.0054
-0.082
-0.0391
0.0482
-0.0048
0.1148
0.1919
0.0047
-0.0487
0.0165
-0.0124
-0.0161
-0.0199
-0.0727
78.6253
2.6382
17.8332
3
0.5184
0.0793
0.5879
0.4138
-0.12
1.0581
-0.0415
0.0426
0.0646
-0.0261
0.0042
-0.0263
-0.0954
0.1345
0.0372
-0.0743
-0.0377
-0.0046
0.0343
-0.0307
-0.0446
89.1974
21.6825
41.9998
4
0.7042
0.0232
0.3135
0.755
0.1101
1.9489
0.0386
-0.0839
-0.1445
-0.127
0.0115
0.0616
0.1234
-0.0781
-0.05
-0.0564
-0.0155
-0.0524
-0.0879
0.0474
-0.0041
42.2981
-0.49
27.5709
5
0.8038
0.0111
-0.0087
0.5766
-0.1644
0.7685
0.0416
0.0161
-0.0567
-0.0599
0.0201
0.0271
0.0598
0.0029
-0.0617
-0.0411
0.0066
-0.0301
-0.0592
0.0154
-0.0295
49.5326
11.8166
20.2739
6
0.4374
0.1328
0.38
0.4829
0.286
1.1296
0.0871
-0.1739
-0.1343
0.0606
0.0159
0.0604
0.2809
-0.1365
-0.103
-0.0416
-0.0462
-0.0504
-0.0298
0.0985
0.0101
47.3825
-5.2237
48.1878
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
0 - 57
2
X-RAY DIFFRACTION
2
A
58 - 240
3
X-RAY DIFFRACTION
3
A
241 - 432
4
X-RAY DIFFRACTION
4
B
0 - 70
5
X-RAY DIFFRACTION
5
B
71 - 238
6
X-RAY DIFFRACTION
6
B
239 - 431
+
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