4Z0P

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADPH and oxalate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WEQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72890.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, 5 mM NADPH, and 50 mM oxalic acid pH=7.0 were mixed with 0.2 ul of the MCSG Suite 2 condition #28 (0.2M Ammonium Citrate Tribasic, anhydrous, 20%w/v PEG 3350 pH=7) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop. Before crystallization, the protein-ligand mixture was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours
Crystal Properties
Matthews coefficientSolvent content
3.9368.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.099α = 90
b = 108.099β = 90
c = 80.226γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2014-11-06MSINGLE 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
11.75099.90.0740.0740.0690.0318.36.960027-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.731000.8520.9380.430.7262.46.72901

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 REPLACEMENTTHROUGHOUT4WEQ1.75056748295499.930.13510.13440.1497RANDOM31.028
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]
0.390.20.39-1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.518
r_dihedral_angle_4_deg13.376
r_dihedral_angle_3_deg11.034
r_dihedral_angle_1_deg5.64
r_mcangle_it3.826
r_mcbond_it3.119
r_mcbond_other3.116
r_angle_refined_deg1.475
r_angle_other_deg0.946
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.518
r_dihedral_angle_4_deg13.376
r_dihedral_angle_3_deg11.034
r_dihedral_angle_1_deg5.64
r_mcangle_it3.826
r_mcbond_it3.119
r_mcbond_other3.116
r_angle_refined_deg1.475
r_angle_other_deg0.946
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2404
Nucleic Acid Atoms
Solvent Atoms429
Heterogen Atoms83

Software

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