5J23

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with 2'-phospho-ADP-ribose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Z0P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72890.2 ul of 13 mg/ml protein in 10 mM NADPH, 10 mM Glycolic Acid, 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 condition #20 (1.1 M Malonic acid, 0.072 M Succinic acid, 0.15M Ammonium dihydrogen citrate, 0.18 M DL-Malic Acid, 0.096 M Ammonium tartrate, 0.24 M Sodium acetate anhydrous, 0.3 M Sodium formate, pH=7.0) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization, the protein was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours.
Crystal Properties
Matthews coefficientSolvent content
3.0159.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.822α = 90
b = 175.822β = 90
c = 136.839γ = 120
Symmetry
Space GroupH 3

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)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
12.3501000.0770.0777.53.970083-345.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.341000.6621.83.9

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 REPLACEMENTTHROUGHOUT4Z0P2.336.6766631343499.910.14750.14640.169RANDOM46.78
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]
-8.99-8.9917.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.241
r_dihedral_angle_4_deg20.554
r_dihedral_angle_3_deg12.775
r_dihedral_angle_1_deg5.437
r_mcangle_it2.02
r_angle_refined_deg1.491
r_mcbond_it1.293
r_mcbond_other1.281
r_angle_other_deg1.21
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.241
r_dihedral_angle_4_deg20.554
r_dihedral_angle_3_deg12.775
r_dihedral_angle_1_deg5.437
r_mcangle_it2.02
r_angle_refined_deg1.491
r_mcbond_it1.293
r_mcbond_other1.281
r_angle_other_deg1.21
r_chiral_restr0.083
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9454
Nucleic Acid Atoms
Solvent Atoms603
Heterogen Atoms179

Software

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