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Crystal structure of 3-hydroxybutylryl-CoA dehydrogenase with acetoacetyl-CoA from Clostridium butyricum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 295 (NH4)2SO4, CAPs, Li2SO4, pH 10.5, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.49 64.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.338 α = 90 b = 146.338 β = 90 c = 409.757 γ = 120
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 2011-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 30 92.6 0.088 11.4 3.6 112292 103800
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 2.5 2.54 81.2 0.306 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.51 29.55 98571 98569 5229 92.44 0.19427 0.19093 0.25738 0.2057 RANDOM 53.767
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] 0.23 0.23 0.23 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.349 r_dihedral_angle_4_deg 20.594 r_dihedral_angle_3_deg 19.824 r_dihedral_angle_1_deg 7.286 r_mcangle_it 5.303 r_scbond_it 4.189 r_mcbond_it 3.572 r_mcbond_other 3.572 r_angle_refined_deg 1.649 r_angle_other_deg 0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.349 r_dihedral_angle_4_deg 20.594 r_dihedral_angle_3_deg 19.824 r_dihedral_angle_1_deg 7.286 r_mcangle_it 5.303 r_scbond_it 4.189 r_mcbond_it 3.572 r_mcbond_other 3.572 r_angle_refined_deg 1.649 r_angle_other_deg 0.807 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it 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 16912 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 270
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction