4NPC

Crystal Structure of an Oxidoreductase, Short-Chain Dehydrogenase/Reductase Family Protein from Brucella suis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EGFPDB entry 4EGF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7289MCSG1(f5): 0.2M Sodium Acetate, 20% PEG-3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0539.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.74α = 90
b = 87.74β = 90
c = 117γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2013-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7570.1999.60.04229.7174670746513-329.873
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.899.90.4934.06

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4EGF1.75504886546512235399.580.15060.14870.1871RANDOM26.4
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.41-0.410.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.712
r_dihedral_angle_4_deg15.373
r_dihedral_angle_3_deg12.819
r_dihedral_angle_1_deg6.092
r_angle_refined_deg1.497
r_mcangle_it1.391
r_mcbond_it0.931
r_mcbond_other0.928
r_angle_other_deg0.809
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.712
r_dihedral_angle_4_deg15.373
r_dihedral_angle_3_deg12.819
r_dihedral_angle_1_deg6.092
r_angle_refined_deg1.497
r_mcangle_it1.391
r_mcbond_it0.931
r_mcbond_other0.928
r_angle_other_deg0.809
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3614
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms8

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction