Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Sequence details
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 22-460 OF THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Citrate pH 5.6, 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
0.97852
1
3
0.97802
1
Reflection
Resolution: 2.11→29.801 Å / Num. obs: 31222 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.599 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.11-2.16
6.4
0.923
1.8
14428
2248
0.923
100
2.16-2.22
6.4
0.749
2.3
14176
2207
0.749
100
2.22-2.29
6.4
0.653
2.6
13776
2148
0.653
100
2.29-2.36
6.4
0.557
3.1
13439
2089
0.557
100
2.36-2.44
6.4
0.481
3.5
12948
2026
0.481
100
2.44-2.52
6.4
0.401
4.2
12638
1970
0.401
100
2.52-2.62
6.4
0.36
4.8
12090
1885
0.36
100
2.62-2.72
6.4
0.271
6
11809
1853
0.271
100
2.72-2.85
6.4
0.198
7.7
11175
1749
0.198
100
2.85-2.98
6.4
0.164
9.4
10801
1692
0.164
100
2.98-3.15
6.4
0.13
11.9
10326
1620
0.13
100
3.15-3.34
6.3
0.103
15.1
9625
1523
0.103
100
3.34-3.57
6.3
0.085
19.2
9114
1445
0.085
100
3.57-3.85
6.3
0.072
22.8
8512
1358
0.072
100
3.85-4.22
6.3
0.06
25.9
7777
1244
0.06
100
4.22-4.72
6.2
0.055
29.2
7059
1146
0.055
100
4.72-5.45
6.1
0.065
29.4
6229
1026
0.065
100
5.45-6.67
6
0.06
27.9
5248
881
0.06
99.9
6.67-9.44
5.8
0.053
28.7
4055
701
0.053
99.3
9.44-29.8
5.2
0.047
29.9
2141
411
0.047
95.1
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0110
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.11→29.801 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.054 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.183 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. 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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. GLYCEROL (GOL) AND ACETATE (ACT) FROM THE CRYOPROTECTION AND CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE. 6. THE SIDECHAIN OF ASN A128 IS NEAR THE INTERFACE BETWEEN SYMMETRY-RELATED MOLECULES AND COULD NOT BE RELIABLY MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.238
1564
5 %
RANDOM
Rwork
0.195
-
-
-
obs
0.197
31147
99.85 %
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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
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