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Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and a substrate D-3-hydroxybutyrate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 30% PEG 4000, 100mM Tris hydrochloride pH 8.0, 200mM D-3-hydroxybutyrate, 5mM NAD+, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.78 α = 90 b = 62.78 β = 90 c = 119.49 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 2011-10-29 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) 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 1.19 33.63 74 11.2 12 57643
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 1.19 24.67 57643 3102 78.26 0.158 0.1572 0.1671 0.1727 0.1816 RANDOM 10.793
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] 0.14 0.14 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.785 r_dihedral_angle_3_deg 13.454 r_dihedral_angle_4_deg 10.837 r_dihedral_angle_1_deg 6.598 r_angle_refined_deg 1.402 r_angle_other_deg 0.672 r_chiral_restr 0.09 r_gen_planes_refined 0.016 r_bond_refined_d 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.785 r_dihedral_angle_3_deg 13.454 r_dihedral_angle_4_deg 10.837 r_dihedral_angle_1_deg 6.598 r_angle_refined_deg 1.402 r_angle_other_deg 0.672 r_chiral_restr 0.09 r_gen_planes_refined 0.016 r_bond_refined_d 0.01 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 234 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling MOLREP phasing