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NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 15-18 % 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 coefficient Solvent content 2.81 56.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.49 α = 90 b = 67.49 β = 90 c = 312.785 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2002-09-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.2545, 1.2555, 1.0500 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.98 20 98.8 0.053 28.17 17.2 30959 28589 2 2 20.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.98 2.031 93.9 0.316 6.84 1728
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.98 19.46 28589 1492 100 0.17966 0.17726 0.1907 0.22532 0.231 RANDOM 20.999
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] 1.09 0.55 1.09 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.943 r_scangle_it 4.712 r_scbond_it 3.042 r_mcangle_it 1.851 r_angle_refined_deg 1.697 r_mcbond_it 1.144 r_angle_other_deg 0.879 r_symmetry_vdw_other 0.319 r_nbd_other 0.257 r_nbd_refined 0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.943 r_scangle_it 4.712 r_scbond_it 3.042 r_mcangle_it 1.851 r_angle_refined_deg 1.697 r_mcbond_it 1.144 r_angle_other_deg 0.879 r_symmetry_vdw_other 0.319 r_nbd_other 0.257 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.121 r_symmetry_vdw_refined 0.091 r_nbtor_other 0.086 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2564 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction XDS data scaling SHARP phasing