Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
Y
Has protein modification
Y
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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG3350, 100 mM imidazole-HCl buffer (pH 7.5), 300 mM zinc acetate, and 50 mM sodium fluoride
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Data collection
Diffraction
Mean temperature: 95 K / Serial crystal experiment: N
Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.12 Å / Relative weight: 1
Reflection
Resolution: 1.6→43.42 Å / Num. obs: 40100 / % possible obs: 90.1 % / Redundancy: 7.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.2
Reflection shell
Resolution: 1.6→1.63 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.039 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 956 / CC1/2: 0.66 / % possible all: 48.4
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0253
refinement
XDS
datareduction
Aimless
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.624 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.245
2014
5 %
RANDOM
Rwork
0.192
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-
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obs
0.195
38053
90.01 %
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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