5V72

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UOGPDB entry 5UOG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52890.2 uL of 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 + 0.2 uL MCSG Suite II condition #9 (0.1 M sodium citrate, pH 5.0, 20% w/v PEG6000), equilibrated against 1.5 M sodium chloride in a 96-well 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 2 mg/mL chymotrypsin solution at 289 K for 3 hours prior to crystallization
Crystal Properties
Matthews coefficientSolvent content
2.244.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.188α = 90
b = 157.926β = 110.74
c = 64.719γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2014-07-25MSINGLE 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
12.15098.40.0960.0960.1150.0626.73.268211-328
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)
12.12.1499.10.4310.4310.5150.2790.8342.33.2

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 REPLACEMENTTHROUGHOUTPDB entry 5UOG2.15064518335098.360.16620.16420.204RANDOM35.344
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]
0.95-1.072.13-1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.347
r_dihedral_angle_4_deg22.175
r_dihedral_angle_3_deg12.873
r_dihedral_angle_1_deg5.904
r_angle_refined_deg1.464
r_angle_other_deg0.978
r_chiral_restr0.082
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.347
r_dihedral_angle_4_deg22.175
r_dihedral_angle_3_deg12.873
r_dihedral_angle_1_deg5.904
r_angle_refined_deg1.464
r_angle_other_deg0.978
r_chiral_restr0.082
r_bond_refined_d0.015
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 Atoms9315
Nucleic Acid Atoms
Solvent Atoms1151
Heterogen Atoms28

Software

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