Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
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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: 3.43 Å3/Da / Density % sol: 63.86 % Description: THE MODEL FROM A SECOND CRYSTAL FORM OF SE-MET CRYSTALS (P 41 2 2, PDB ID 2EVR) WAS USED AS A STARTING MODEL TO SPEED UP THE REFINEMENT. THE STRUCTURE CAN BE SOLVED BY SE-MAD. MORE THAN ...Description: THE MODEL FROM A SECOND CRYSTAL FORM OF SE-MET CRYSTALS (P 41 2 2, PDB ID 2EVR) WAS USED AS A STARTING MODEL TO SPEED UP THE REFINEMENT. THE STRUCTURE CAN BE SOLVED BY SE-MAD. MORE THAN 90 PERCENT OF PROTEIN MODELS CAN BE AUTOMATICALLY TRACED FROM EXPERIMENTAL PHASES ONLY.
Crystal grow
Temperature: 277 K / pH: 7.5 Details: 1.4M Na3Citrate, 0.1M HEPES, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 7.5
Resolution: 1.79→29.48 Å / Num. obs: 72488 / % possible obs: 97.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 12.56
Reflection shell
Rmerge(I) obs: 0.01146 / Diffraction-ID: 1
Resolution (Å)
% possible obs (%)
Redundancy (%)
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.79-1.86
89.4
6.5
2.13
85045
11630
89.4
1.86-1.94
95.1
2.72
107459
14142
1.94-2.03
97
3.91
104199
13659
2.03-2.13
97.7
5.18
96775
12690
2.13-2.27
98.6
6.49
109814
14348
2.27-2.44
99
8.57
102198
13295
2.44-2.69
99.2
10.87
107820
14008
2.69-3.07
99.5
16.27
104438
13539
3.07-3.87
99.9
28.08
107375
13953
3.87-29.48
99.6
39.07
106847
13941
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
XSCALE
datascaling
PDB_EXTRACT
1.601
dataextraction
XDS
datareduction
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.79→29.48 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.612 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076 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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE DIFFERENCE DENSITY MAP NEAR A/B 116 IS NOISY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.172
3659
5.1 %
RANDOM
Rwork
0.154
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-
-
all
0.155
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-
-
obs
-
68770
99.55 %
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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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