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Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor methylmalonate
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 4.4 293 34% PEG 4000, 100mM Tris hydrochloride, 200mM sodium methylmalonate, 5mM NAD+, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.74 α = 90 b = 62.74 β = 90 c = 119.22 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 1.00 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 1.37 22.92 98.64 50566 50566
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 1.37 1.44 98.05
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 1.37 22.92 50489 49937 5084 98.91 0.15805 0.15507 0.1534 0.18435 0.1822 RANDOM 13.065
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 37.373 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_4_deg 12.16 r_dihedral_angle_1_deg 6.213 r_scangle_it 5.308 r_scbond_it 3.279 r_angle_refined_deg 2.447 r_mcangle_it 1.999 r_mcbond_it 1.271 r_chiral_restr 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.373 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_4_deg 12.16 r_dihedral_angle_1_deg 6.213 r_scangle_it 5.308 r_scbond_it 3.279 r_angle_refined_deg 2.447 r_mcangle_it 1.999 r_mcbond_it 1.271 r_chiral_restr 0.166 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 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_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 305 Heterogen Atoms 56
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling