5UNN

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in apo form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62890.2 ul of 12 mg/ml protein in 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 I condition # 88 (0.1 M Sodium citrate pH=5.6, 20% v/v 2-Propanol, 20% w/v PEG 4000 ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci)
Crystal Properties
Matthews coefficientSolvent content
3.6666.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.592α = 90
b = 128.592β = 90
c = 122.847γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2015-04-18MSINGLE 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
12501000.1080.1080.1170.0446.96.967353-328.5
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)
122.031000.9020.9020.9860.3890.6151.76.6

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 REPLACEMENTTHROUGHOUT4Z0P25063691351799.860.14820.14680.1742RANDOM44.268
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]
-0.19-0.190.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.372
r_dihedral_angle_4_deg19.916
r_dihedral_angle_3_deg11.181
r_dihedral_angle_1_deg5.6
r_angle_refined_deg1.369
r_angle_other_deg0.927
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.372
r_dihedral_angle_4_deg19.916
r_dihedral_angle_3_deg11.181
r_dihedral_angle_1_deg5.6
r_angle_refined_deg1.369
r_angle_other_deg0.927
r_chiral_restr0.083
r_bond_refined_d0.011
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 Atoms3424
Nucleic Acid Atoms
Solvent Atoms659
Heterogen Atoms13

Software

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