Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT (RESIDUES 18-228) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 18-228) 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10.00% 2-propanol, 20.00% polyethylene glycol 4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.37→29.552 Å / Num. all: 93097 / Num. obs: 93097 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rsym value: 0.093 / Net I/σ(I): 7.2
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
1.37-1.41
3.5
0.88
0.8
23690
6832
0.88
99.5
1.41-1.44
3.5
0.702
1
23101
6664
0.702
99.8
1.44-1.49
3.5
0.516
1.4
22530
6476
0.516
99.8
1.49-1.53
3.5
0.396
1.8
22135
6301
0.396
99.8
1.53-1.58
3.5
0.333
2.1
21450
6075
0.333
99.6
1.58-1.64
3.5
0.264
2.7
20962
5914
0.264
99.5
1.64-1.7
3.6
0.221
3.3
20340
5694
0.221
99.3
1.7-1.77
3.6
0.175
4.1
19586
5461
0.175
99.1
1.77-1.85
3.6
0.143
5
18823
5246
0.143
99.1
1.85-1.94
3.6
0.119
5.9
18063
5045
0.119
99.1
1.94-2.04
3.6
0.101
6.7
17075
4784
0.101
99.3
2.04-2.17
3.5
0.091
7.4
16170
4573
0.091
99.5
2.17-2.32
3.5
0.086
7.6
15231
4307
0.086
99.6
2.32-2.5
3.5
0.083
7.8
13994
4023
0.083
99.7
2.5-2.74
3.4
0.081
7.8
12783
3723
0.081
99.7
2.74-3.06
3.3
0.072
9
11209
3353
0.072
98.7
3.06-3.54
3.3
0.061
10.5
9687
2963
0.061
99.3
3.54-4.33
3.6
0.05
12.9
9243
2544
0.05
99.4
4.33-6.13
3.6
0.046
13.8
7191
1998
0.046
98.8
6.13-29.552
3.4
0.042
15
3865
1121
0.042
95.8
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
SCALA
3.3.20
datascaling
REFMAC
5.5.0110
refinement
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.37→29.552 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 1.766 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CHLORIDE (CL) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION/CRYO CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE. 4.UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED INTO THE PUTATIVE ACTIVE SITE.IDENTIFICATION OF THE PUTATIVE ACTIVE SITE IS BASED ON ElECTRON DENSITY AND STRUCTURAL COMPARISONS WITH SIMILAR PROTEINS OF KNOWN FUNCTION. 5.THE SIDECHAINS OF GLU B177,ASP B193,GLU A211, AND GLU B33 SHOW ELEVATED NEGATIVE DIFFERENCE DENSITY. THE OCCUPANCIES OF THE SIDECHAIN ATOMS WERE NOT ADJUSTED IN THESE REGIONS OF APPARENT RADIATION DAMAGE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1732
4655
5 %
RANDOM
Rwork
0.1337
-
-
-
obs
0.1356
92858
99.03 %
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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: BABINET MODEL WITH MASK
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