Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.37 Å3/Da / Density % sol: 48 % Description: THE RMERGE AND STATISTICS REPORTED HERE BY XSCALE ARE BASED ON TREATING FRIEDEL PAIRS AS SEPARATE REFLECTIONS.
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 3.2M ammonium sulfate, 0.1M Bicine pH 9.0, 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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979032 Å / Relative weight: 1
Reflection
Resolution: 1.52→27.146 Å / Num. obs: 25437 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.97 % / Biso Wilson estimate: 15.026 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.44
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.52-1.57
0.443
2.1
9028
4403
1
98.3
1.57-1.64
0.341
2.7
11114
5366
1
99.1
1.64-1.71
0.25
3.7
9422
4517
1
99.3
1.71-1.8
0.185
4.9
10104
4838
1
99.1
1.8-1.91
0.128
7.1
9838
4705
1
99
1.91-2.06
0.08
10.4
10367
4924
1
98.8
2.06-2.27
0.052
15.3
10262
4862
1
99.2
2.27-2.6
0.039
19.2
10227
4828
1
98.8
2.6-3.27
0.03
24.5
10046
4739
1
98
3.27-27.146
0.019
34.4
10227
4791
1
98
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
Refinement
Method to determine structure: SAD / Resolution: 1.52→27.146 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.247 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.067 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 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 ...Details: 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 HAVE BEEN MODELED IN TWO CONFORMATIONS. THE PEPTIDE LINKING THE PANTHOTHENATE AND BETA-MERCAPTOETHYLAMINE IN CONFORMER A HAS BEEN BUILT IN A DIFFERENT ORIENTATION THAT IN THE MODEL FOR THE RELATED PH 6 STRUCTURE. WHILE THIS APPEARS PLAUSIBLE, GIVEN THE AMBIGUITY IN THE DENSITY FOR THIS REGION, NO CONCLUSIONS SHOULD BE DRAWN WITH HIGH CONFIDENCE. 6. FOUR SULFATE IONS AND TWO GLYCEROL MOLECULES FROM THE CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE. ONE OF THE SULFATE MOLECULES, A204, WAS MODELED WITH PARTIAL OCCUPANCY IN TWO ALTERNATE POSITIONS AT THE PUTATIVE ACTIVE SITE. ASSIGNMENT OF THIS ELECTRON DENSITY TO A DISORDERED SULFATE IS TENTATIVE. 7. LOOPS 131-134 and 70-73 ARE DISORDERED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.178
1301
5.1 %
RANDOM
Rwork
0.16
-
-
-
obs
0.161
25434
99.74 %
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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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