4JVV

Crystal structure of the evolved variant of the computationally designed serine hydrolase, OSH55.4_H1, covalently bound with diisopropyl fluorophosphate (DFP), Northeast Structural Genomics Consortium (NESG) Target OR273


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Under Oil
pH 10
Temperature 277.0
Details Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: NH4Cl 0.1M, CAPS 0.1M, PEG400 40%, microbatch under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.15 α = 90
b = 67.67 β = 94.35
c = 37.54 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2012-11-20
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.97894 NSLS X4A

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.29 50 98.8 0.071 -- -- 7.3 -- 7903 -- -3.0 20.09

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.288 26.58 -- 1.44 -- 7594 370 95.27 -- 0.195 0.192 0.244 random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.288 2.619 -- 114 2226 0.214 0.309 -- 89.0
X Ray Diffraction 2.619 3.298 -- 128 2519 0.205 0.307 -- 100.0
X Ray Diffraction 3.298 26.582 -- 128 2479 0.177 0.189 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.035
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.11
f_plane_restr 0.005
f_chiral_restr 0.08
f_angle_d 1.193
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1177
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 93

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
BALBES Structure Solution
PHENIX (phenix.refine: 1.8.2_1296) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement