5BQF

Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L(+)-tartaric acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.53000.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP 10 mM NADP were mixed with 0.2 ul of the MCSG Suite 2 condition #71 (0.2M Na tartrate, 20%w/v PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization the protein was incubated with 1/50 v/v of 2 mg/ml TEV solution
Crystal Properties
Matthews coefficientSolvent content
2.3246.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.692α = 90
b = 65.692β = 90
c = 151.406γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300CCDADSC QUANTUM 315r2014-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
11.455097.50.0630.0630.0720.03510.9458208-315.6
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)
11.451.4899.50.5470.6330.3130.7591.93.92905

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 REPLACEMENTTHROUGHOUT4xcv1.455055340285797.570.13980.13850.1654RANDOM19.704
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]
0.020.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.187
r_dihedral_angle_4_deg15.658
r_dihedral_angle_3_deg11.446
r_sphericity_bonded9.285
r_dihedral_angle_1_deg5.539
r_rigid_bond_restr2.954
r_mcangle_it2.221
r_mcbond_it1.759
r_mcbond_other1.759
r_angle_refined_deg1.441
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.187
r_dihedral_angle_4_deg15.658
r_dihedral_angle_3_deg11.446
r_sphericity_bonded9.285
r_dihedral_angle_1_deg5.539
r_rigid_bond_restr2.954
r_mcangle_it2.221
r_mcbond_it1.759
r_mcbond_other1.759
r_angle_refined_deg1.441
r_angle_other_deg0.943
r_chiral_restr0.083
r_bond_refined_d0.008
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 Atoms2476
Nucleic Acid Atoms
Solvent Atoms487
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000phasing
Cootmodel building
MOLREPphasing
HKL-3000data scaling
HKL-3000data reduction
HKL-3000data collection