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Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and a substrate D-3-hydroxybutyrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 30% PEG4000, 100mM Tris hydrochloride, 200mM D-3-hydroxybutyrate, 5mM NAD+, pH 8.0, 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 1.00 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 75.23 51382 51382
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.24 1.31 66.63
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 3VDR 1.24 18.98 51224 46108 5116 74.89 0.16793 0.16523 0.1652 0.19223 0.1919 RANDOM 10.078
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.059 r_dihedral_angle_4_deg 14.458 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 6.291 r_scangle_it 4.827 r_scbond_it 3.058 r_angle_refined_deg 2.415 r_mcangle_it 2.076 r_mcbond_it 1.301 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.059 r_dihedral_angle_4_deg 14.458 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 6.291 r_scangle_it 4.827 r_scbond_it 3.058 r_angle_refined_deg 2.415 r_mcangle_it 2.076 r_mcbond_it 1.301 r_chiral_restr 0.156 r_bond_refined_d 0.029 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1906 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 52
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling