Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
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. THE CLONED CONSTRUCT CONTAINS RESIDUES 25-414 OF THE FULL LENGTH PROTEIN.
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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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: NANODROP, 20.0% PEG 6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.9→29.399 Å / Num. obs: 44914 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 18.609 Å2 / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 4.824
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.9-1.95
7.2
0.778
1
23246
3207
0.778
100
1.95-2
7.2
0.681
1.1
22813
3160
0.681
100
2-2.06
7.3
0.566
1.3
22307
3071
0.566
100
2.06-2.12
7.2
0.459
1.6
21585
2991
0.459
100
2.12-2.19
7.3
0.377
2
20992
2894
0.377
100
2.19-2.27
7.2
0.328
1.7
20315
2817
0.328
100
2.27-2.36
7.2
0.287
2.6
19768
2732
0.287
100
2.36-2.45
7.2
0.24
3.1
19068
2640
0.24
100
2.45-2.56
7.2
0.207
3.6
18058
2509
0.207
100
2.56-2.69
7.2
0.179
4.2
17477
2432
0.179
100
2.69-2.83
7.2
0.152
5
16614
2315
0.152
100
2.83-3
7.1
0.123
6
15717
2210
0.123
100
3-3.21
7.1
0.102
7.2
14758
2077
0.102
100
3.21-3.47
7.1
0.079
8.8
13883
1968
0.079
100
3.47-3.8
7
0.061
11.1
12715
1807
0.061
100
3.8-4.25
6.9
0.056
11.5
11450
1648
0.056
100
4.25-4.91
6.8
0.055
11.9
10098
1475
0.055
100
4.91-6.01
6.7
0.06
10.5
8548
1283
0.06
100
6.01-8.5
6.4
0.061
10.5
6671
1041
0.061
100
8.5-29.399
5.5
0.053
10.8
3487
637
0.053
97.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.9→29.399 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.81 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.12 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. PEG MOLECULES FROM CRYSTALLIZATION AND ETHYLENE GLYCOL FROM CRYOPROTECTION ARE MODELED IN THIS STRUCTURE. 4. UNKNOWN ELECTRON DENSITY IS OBSERVED AND UNMODELED NEAR SER 256 AND HIS 398.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.209
2257
5 %
RANDOM
Rwork
0.168
-
-
-
obs
0.17
44778
100 %
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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: BABINET MODEL WITH MASK
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