Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
-
Details
Has protein modification
Y
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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.
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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: 2.4 Å3/Da / Density % sol: 48.77 %
Resolution: 1.8→28.961 Å / Num. obs: 27317 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.535 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.95
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.8-1.86
0.695
1.3
9109
4681
96.6
1.86-1.94
0.493
1.9
10710
5475
98.7
1.94-2.03
0.345
2.7
10254
5211
99
2.03-2.13
0.258
3.4
9378
4781
98.8
2.13-2.27
0.175
4.7
10594
5366
98.9
2.27-2.44
0.13
6
9748
4950
98.9
2.44-2.69
0.097
7.8
10338
5219
98.9
2.69-3.07
0.066
10.9
9918
4999
98.9
3.07-3.87
0.039
17.4
10266
5135
98.2
3.87
0.032
23.5
10195
5019
96.1
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0102
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→45.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.789 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.113 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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE METAL PRESENT IN THE PUTATIVE ACTIVE SITE WAS TENTATIVELY ASSIGNED AS NICKLE (NI) BASED ON X-RAY FLURORESCENCE SPECTROSCOPY AND ANOMALOUS DIFFERENCE FOURIERS. NICKLE IONS WERE PRESENT DURING PURIFICATION AS CHELATING AGENT. 5. GLYCEROL (GOL), SULFATE (SO4) AND POLYETHYLENE GLYCOL FRAGMENTS (PEG AND PG4) MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.207
1366
5 %
RANDOM
Rwork
0.173
-
-
-
obs
0.175
27263
99.21 %
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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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