5V7G

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADPH and oxalate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5J23PDB entry 5J23

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52890.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADPH, 50 mM oxalic acid, pH 7.0 + 0.2 uL TOP96 condition #41 (0.1 M sodium cacodylate, pH 6.5, 18% w/v PEG8000, 0.2 M sodium acetate), equilibrated against 1.5 M sodium chloride in a 96-well, 3-drop crystallization plate (Swissci), incubated with 1/20 v/v 1 mg/mL rTEV at 289 K for 3 hours prior to crystallization
Crystal Properties
Matthews coefficientSolvent content
2.9858.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.209α = 90
b = 178.209β = 90
c = 133.799γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2015-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.755098.80.0810.0810.0920.0437.94.5157652-326.4
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)
11.751.7899.70.6670.6670.760.3590.7832.14.37958

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 REPLACEMENTTHROUGHOUTPDB entry 5J231.7537.07149734789698.810.15140.14980.1801RANDOM31.43
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]
-4.97-4.979.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.061
r_dihedral_angle_4_deg21.012
r_dihedral_angle_3_deg11.592
r_dihedral_angle_1_deg5.788
r_angle_refined_deg1.46
r_angle_other_deg0.969
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.061
r_dihedral_angle_4_deg21.012
r_dihedral_angle_3_deg11.592
r_dihedral_angle_1_deg5.788
r_angle_refined_deg1.46
r_angle_other_deg0.969
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9429
Nucleic Acid Atoms
Solvent Atoms1804
Heterogen Atoms242

Software

Software
Software NamePurpose
MD2data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling