5V7N

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADP and 2-Keto-D-gluconic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.92890.2 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, 100 mM 2-keto-D-gluconic acid hemicalcium salt + 0.2 uL TOP96 condition #24 (0.2 M magnesium formate, pH 5.9, 20% w/v PEG3350), 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
2.9358.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.902α = 90
b = 175.902β = 90
c = 135.336γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium Lenses2016-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.755099.60.1130.1130.1290.068.64.9156897-328.1
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)
11.751.781000.8780.8780.9870.4470.6071.84.97876

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 5J231.7545.11148739783699.420.14510.14390.1666RANDOM32.918
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]
1.051.05-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.506
r_dihedral_angle_4_deg20.039
r_dihedral_angle_3_deg11.1
r_dihedral_angle_1_deg5.786
r_angle_refined_deg1.502
r_angle_other_deg0.999
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.506
r_dihedral_angle_4_deg20.039
r_dihedral_angle_3_deg11.1
r_dihedral_angle_1_deg5.786
r_angle_refined_deg1.502
r_angle_other_deg0.999
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9468
Nucleic Acid Atoms
Solvent Atoms1350
Heterogen Atoms301

Software

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