Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT INCLUDING RESIDUES 25-467 WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...THIS CONSTRUCT INCLUDING RESIDUES 25-467 WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2000M MgCl2, 30.0000% PEG-400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97791
1
Reflection
Resolution: 1.7→29.374 Å / Num. obs: 58230 / % possible obs: 97.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 10.978 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 7.9
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
1.7-1.74
2.6
0.462
1.9
11090
4239
0.462
96
1.74-1.79
2.6
0.401
2.2
10784
4117
0.401
96.1
1.79-1.84
2.6
0.331
2.7
10562
4025
0.331
96.4
1.84-1.9
2.6
0.288
3.2
10261
3920
0.288
96.6
1.9-1.96
2.6
0.241
4
9961
3800
0.241
96.8
1.96-2.03
2.6
0.203
4.8
9600
3671
0.203
97
2.03-2.11
2.6
0.174
5.7
9448
3618
0.174
97.2
2.11-2.19
2.6
0.155
6.5
8899
3400
0.155
97.3
2.19-2.29
2.6
0.137
7.4
8802
3370
0.137
97.6
2.29-2.4
2.6
0.12
8.3
8212
3158
0.12
97.9
2.4-2.53
2.6
0.109
9.2
7843
3010
0.109
97.8
2.53-2.69
2.6
0.101
10.1
7431
2854
0.101
98.1
2.69-2.87
2.6
0.09
11.3
7019
2697
0.09
98.2
2.87-3.1
2.6
0.078
13.3
6604
2547
0.078
98.4
3.1-3.4
2.6
0.07
15.3
5985
2308
0.07
98.6
3.4-3.8
2.6
0.063
17.2
5434
2114
0.063
98.7
3.8-4.39
2.6
0.066
18.6
4842
1865
0.066
99
4.39-5.38
2.6
0.069
18.8
4069
1587
0.069
99.2
5.38-7.6
2.5
0.08
16.7
3165
1251
0.08
99.4
7.6-29.37
2.5
0.063
20
1693
679
0.063
97.7
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0053
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.7→29.374 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.559 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.086 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.ZINC (ZN) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON A FLUORESCENCE EXCITATION SCAN AND THE ANOMALOUS DIFFERENCE FOURIER MAP. 5.THERE IS A CIS-PEPTIDE BOND BETWEEN RESIDUES ASP292 AND ASP293 AT THE PUTATIVE ACTIVE SITE. 6.PEG FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.182
2960
5.1 %
RANDOM
Rwork
0.151
-
-
-
obs
0.152
58229
97.26 %
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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
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