1XDW

NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729015-18 % PEG MME 2000 or PEG 2000, and 0.2 M sodium or lithium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.8156.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.49α = 90
b = 67.49β = 90
c = 312.785γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2002-09-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.2545, 1.2555, 1.0500MPG/DESY, HAMBURGBW6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.982098.80.05328.1717.230959285892220.99
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.982.03193.90.3166.841728

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.9819.462858914921000.179660.177260.22532RANDOM20.999
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]
1.090.551.09-1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.943
r_scangle_it4.712
r_scbond_it3.042
r_mcangle_it1.851
r_angle_refined_deg1.697
r_mcbond_it1.144
r_angle_other_deg0.879
r_symmetry_vdw_other0.319
r_nbd_other0.257
r_nbd_refined0.241
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.943
r_scangle_it4.712
r_scbond_it3.042
r_mcangle_it1.851
r_angle_refined_deg1.697
r_mcbond_it1.144
r_angle_other_deg0.879
r_symmetry_vdw_other0.319
r_nbd_other0.257
r_nbd_refined0.241
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.174
r_chiral_restr0.121
r_symmetry_vdw_refined0.091
r_nbtor_other0.086
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2564
Nucleic Acid Atoms
Solvent Atoms403
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
XDSdata scaling
SHARPphasing