4XCV

Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KBO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52890.2 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 and 10 mM glycolic acid were mixed with 0.2 ul of the MCSG-I condition #45 (0.2 M Sodium Chloride, 0.1 M Tris:HCl pH 8.5, 25% (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 at 289 K.
Crystal Properties
Matthews coefficientSolvent content
2.346.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.663α = 90
b = 65.663β = 90
c = 151.458γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97912APS19-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
11.45094.80.0670.0670.0720.02510.36.862557-313.8
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)
11.41.42890.9140.9860.3610.7772.16.42891

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 REPLACEMENTTHROUGHOUT3KBO1.45059503310494.870.15070.14930.1775RANDOM20.534
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]
0.40.4-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.159
r_dihedral_angle_4_deg15.329
r_dihedral_angle_3_deg11.633
r_dihedral_angle_1_deg5.414
r_angle_refined_deg1.748
r_mcangle_it1.106
r_angle_other_deg1.07
r_mcbond_it0.699
r_mcbond_other0.699
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.159
r_dihedral_angle_4_deg15.329
r_dihedral_angle_3_deg11.633
r_dihedral_angle_1_deg5.414
r_angle_refined_deg1.748
r_mcangle_it1.106
r_angle_other_deg1.07
r_mcbond_it0.699
r_mcbond_other0.699
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2473
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms55

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
MOLREPphasing
HKL-3000data scaling
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction