5UOG

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5J23 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.52890.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 5 mM NADPH were mixed with 0.2 ul of the MCSG Suite 3 condition #61 (0.1 M Citric acid pH=3.5, 2 M Ammonium sulfate) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). The protein was crystallized with the His-tag
Crystal Properties
Matthews coefficientSolvent content
2.957.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.583α = 90
b = 176.583β = 90
c = 135.008γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97924APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.4501000.0610.0610.0730.049.83.261899-356.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.441000.630.630.7610.4220.68523.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5J232.436.7858425293999.930.13810.13550.1904RANDOM57.536
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]
-12.97-12.9725.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.688
r_dihedral_angle_4_deg20.002
r_dihedral_angle_3_deg13.657
r_dihedral_angle_1_deg5.533
r_angle_refined_deg1.319
r_angle_other_deg1.132
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.688
r_dihedral_angle_4_deg20.002
r_dihedral_angle_3_deg13.657
r_dihedral_angle_1_deg5.533
r_angle_refined_deg1.319
r_angle_other_deg1.132
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9325
Nucleic Acid Atoms
Solvent Atoms972
Heterogen Atoms25

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction