Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Sequence details
1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. 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. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 40.0000% polyethylene glycol 600, 0.1M sodium citrate pH 5.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
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
0.9786
1
3
0.97806
1
Reflection
Resolution: 1.9→28.904 Å / Num. obs: 34930 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 21.874 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 11.9
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
1.9-1.95
7.4
0.986
0.8
18804
2539
0.986
100
1.95-2
7.4
0.781
1
18483
2491
0.781
100
2-2.06
7.4
0.606
1.3
17819
2396
0.606
100
2.06-2.12
7.4
0.513
1.5
17432
2347
0.513
100
2.12-2.19
7.4
0.42
1.8
17031
2294
0.42
100
2.19-2.27
7.5
0.355
2.1
16431
2205
0.355
100
2.27-2.36
7.4
0.304
2.5
15735
2113
0.304
100
2.36-2.45
7.4
0.268
2.8
15360
2072
0.268
100
2.45-2.56
7.5
0.213
3.6
14749
1975
0.213
100
2.56-2.69
7.4
0.18
4.2
14061
1896
0.18
100
2.69-2.83
7.4
0.157
4.8
13379
1804
0.157
100
2.83-3
7.4
0.133
5.5
12642
1710
0.133
100
3-3.21
7.4
0.107
6.6
11820
1598
0.107
100
3.21-3.47
7.3
0.086
4.1
11082
1510
0.086
100
3.47-3.8
7.3
0.066
9.8
10242
1395
0.066
100
3.8-4.25
7.3
0.057
10.5
9232
1271
0.057
100
4.25-4.91
7.2
0.062
10.3
8209
1134
0.062
100
4.91-6.01
7.1
0.07
8.4
6886
967
0.07
100
6.01-8.5
7
0.049
12.4
5313
762
0.049
100
8.5-28.91
6.3
0.048
11.2
2844
451
0.048
97.6
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Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0053
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.9→28.904 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.507 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.118 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. POLY ETHYLENE GLYCOL FRAGMENTS (PGE, P6G) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.206
1752
5 %
RANDOM
Rwork
0.167
-
-
-
obs
0.169
34930
99.94 %
-
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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