(5R)-5-hydroxy-3-methylfuran-2(5H)-one / AB hydrolase-1 domain-containing protein / AB hydrolase-1 domain-containing protein Similarity search - Component
Biological species
Oryza glumipatula (plant)
Method
X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.393 Å
Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O
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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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.02 M amino acid mixture (Glu, Ala, Gly, Lys, and Ser); imidazole; 0.1 M MES monohydrate, pH 6.5, 40% glycerol, 20% PEG4000
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.393→44.158 Å / Num. obs: 115751 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 26.31 Å2 / Rsym value: 0.172 / Net I/σ(I): 60.1
Reflection shell
Resolution: 2.393→2.479 Å / Rsym value: 0.699
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Processing
Software
Name
Version
Classification
PHENIX
1.8.4_1496
refinement
HKL-2000
datascaling
PDB_EXTRACT
3.24
dataextraction
HKL-2000
datareduction
MOLREP
phasing
Refinement
Resolution: 2.393→44.158 Å / FOM work R set: 0.7001 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.19 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.306
1990
1.72 %
Rwork
0.2473
113562
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obs
0.2483
115552
99.67 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL