5V6Q

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72890.2 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 NADP + 0.2 uL MCSG Suite II condition #20 (1.1 M malonic acid, 0.072 M succinic acid, 0.15 M ammonium citrate tribasic, 0.18 M DL-malic acid, 0.096 M ammonium tartrate dibasic, 0.24 M sodium acetate, 0.3 M sodium formate, pH 7), equilibrated against 1.5 M sodium chloride in a 96-well, 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 1 mg/mL rTEV at 289 K for 3 hours prior to crystallization
Crystal Properties
Matthews coefficientSolvent content
2.9658.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.484α = 90
b = 176.484β = 90
c = 135.857γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2014-07-24MSINGLE 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
11.955099.60.1050.1050.1190.0557.64.6114355-330
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)
11.951.9898.60.6910.6910.7840.3660.6862.14.55653

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 5J231.9540.29108794555999.540.14440.14380.1565RANDOM33.875
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]
-2.22-2.224.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.507
r_dihedral_angle_4_deg20.3
r_dihedral_angle_3_deg11.866
r_dihedral_angle_1_deg5.94
r_angle_refined_deg1.34
r_angle_other_deg1.1
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.507
r_dihedral_angle_4_deg20.3
r_dihedral_angle_3_deg11.866
r_dihedral_angle_1_deg5.94
r_angle_refined_deg1.34
r_angle_other_deg1.1
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9446
Nucleic Acid Atoms
Solvent Atoms841
Heterogen Atoms223

Software

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