Mass: 18.015 Da / Num. of mol.: 149 / 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.
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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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 3.2M ammonium sulfate, 0.1M MES pH 6.0, Additive: 0.001 M acetyl Co-enzyme A, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Single crystal Si(311) 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
0.979394
1
3
0.978882
1
Reflection
Resolution: 1.62→27.896 Å / Num. obs: 20813 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.242 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.3
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
1.62-1.66
4
0.668
1.9
6086
1514
0.668
98.4
1.66-1.71
4
0.549
2.4
5911
1466
0.549
98.4
1.71-1.76
4
0.462
2.9
5803
1443
0.462
98.7
1.76-1.81
4
0.356
3.8
5572
1392
0.356
98.7
1.81-1.87
4
0.291
4.6
5412
1354
0.291
98.9
1.87-1.94
3.9
0.34
5.2
5030
1299
0.34
98.8
1.94-2.01
4
0.176
7.4
5041
1273
0.176
98.8
2.01-2.09
3.9
0.133
9.7
4822
1224
0.133
99.4
2.09-2.18
3.9
0.105
12
4625
1179
0.105
99.5
2.18-2.29
3.7
0.145
12.2
4180
1125
0.145
98.6
2.29-2.41
3.9
0.082
15.7
4218
1072
0.082
99.7
2.41-2.56
3.9
0.069
17.7
4028
1036
0.069
99.4
2.56-2.74
3.9
0.067
18.9
3707
959
0.067
99.8
2.74-2.96
3.8
0.061
21.7
3461
911
0.061
99.7
2.96-3.24
3.7
0.053
25.5
3134
837
0.053
99.8
3.24-3.62
3.7
0.045
28.8
2773
756
0.045
99
3.62-4.18
3.3
0.045
29.3
2197
663
0.045
98.3
4.18-5.12
3.9
0.038
34.6
2272
584
0.038
99.9
5.12-7.24
3.8
0.042
32.4
1715
455
0.042
99.9
7.24-27.9
3.4
0.037
31.6
924
271
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
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.62→27.896 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 3.851 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.092 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. 5. ACETYL COENZYME A WAS INCLUDED AS AN ADDITIVE FOR CRYSTALLIZATION. WE SEE NO DENSITY FOR THE ACETYL GROUP AND HAVE MODELED IT IN THE STRUCTURE AS COENZYME A. THE PANTHOTHENATE AND BETA-MERCAPTOETHYLAMINE MOIETIES OF THE CO-A ARE DISORDERED AND A DOMINANT CONFORMATION HAS BEEN MODELED. THE PEPTIDE LINKING THE PANTHOTHENATE AND BETA-MERCAPTOETHYLAMINE IN CONFORMER A HAS BEEN BUILT IN A DIFFERENT ORIENTATION THAN IN THE MODEL FOR THE RELATED PH 9 STRUCTURE. WHILE THIS APPEARS PLAUSIBLE, GIVEN THE AMBIGUITY IN THE DENSITY FOR THIS REGION, NO CONCLUSIONS SHOULD BE DRAWN WITH HIGH CONFIDENCE. 6. THREE SULFATE IONS AND ONE ETHYLENE GLYCOL MOLECULE FROM THE CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.204
1069
5.1 %
RANDOM
Rwork
0.179
-
-
-
obs
0.18
20778
98.6 %
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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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