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Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor methylmalonate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 34% PEG 4000, 100mM Tris hydrochloride pH 8.5, 200mM sodium methylmalonate, 5mM NAD+, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.77 α = 90 b = 62.77 β = 90 c = 119.31 γ = 90
Symmetry Space Group P 42 21 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 CCD ADSC QUANTUM 315r 2011-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.5 22.9 98.7 0.083 22.2 13.3 38406
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 99.1 0.294 2.6 12.7
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 THROUGHOUT 1.5 21.03 34501 3820 98.19 0.1419 0.1396 0.1396 0.1626 0.1626 RANDOM 13.692
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] 0.16 0.16 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.012 r_dihedral_angle_3_deg 14.482 r_dihedral_angle_4_deg 10.547 r_dihedral_angle_1_deg 6.777 r_angle_refined_deg 1.162 r_angle_other_deg 0.631 r_chiral_restr 0.076 r_gen_planes_refined 0.015 r_bond_refined_d 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.012 r_dihedral_angle_3_deg 14.482 r_dihedral_angle_4_deg 10.547 r_dihedral_angle_1_deg 6.777 r_angle_refined_deg 1.162 r_angle_other_deg 0.631 r_chiral_restr 0.076 r_gen_planes_refined 0.015 r_bond_refined_d 0.006 r_gen_planes_other 0.002 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1906 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 56
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing