Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 5.21 Å3/Da / Density % sol: 76 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Drops were set up by mixing polymerase (5.8 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 70% Morpheus G2 (10% w/v PEG 8000, 20% v/v ...Details: Drops were set up by mixing polymerase (5.8 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 70% Morpheus G2 (10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium l-tartrate, 0.2 M sodium oxamate), 0.1 M MES/imidazole) in a 2:1 protein:precipitant ratio.
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
Diamond
I03
1
0.9763
SYNCHROTRON
Diamond
I03
2
1.035
Detector
Type
ID
Detector
Date
DECTRIS PILATUS 6M
1
PIXEL
Feb 2, 2015
DECTRIS PILATUS 6M
2
PIXEL
Apr 14, 2014
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.9763
1
2
1.035
1
Reflection
Resolution: 3.9→100.57 Å / Num. obs: 95267 / % possible obs: 98.8 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.201 / Net I/σ(I): 13.2
Reflection shell
Resolution: 3.9→4 Å / Redundancy: 20.6 % / Rmerge(I) obs: 3.685 / Mean I/σ(I) obs: 1.3 / % possible all: 96.9
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0103
refinement
xia2
datareduction
PHENIX
phasing
SHELX
phasing
Aimless
datascaling
Refinement
Method to determine structure: SIRAS / Resolution: 3.9→50.01 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.912 / SU B: 80.769 / SU ML: 0.987 / Cross valid method: THROUGHOUT / ESU R Free: 0.805 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.32572
4770
5 %
RANDOM
Rwork
0.28578
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-
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obs
0.2878
90335
98.75 %
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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