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Crystal structure of (S)-3-hydroxybutylryl-CoA dehydrogenase form the n-butanol sysnthesizing bacterium, Clostridium butyricum.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F0Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 295 2M (NH4)2SO4,CAPs,Li2SO4, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.42 64.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.475 α = 90 b = 146.475 β = 90 c = 202.295 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 210 2014-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.23985 PAL/PLS 7A (6B, 6C1)
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 1.8 30.9 149905 138509
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 1.8 30.9
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 1F0Y 1.8 30.9 149905 138506 6846 92.4 0.2085 0.2069 0.2152 0.2399 0.2468 RANDOM 35.919
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.875 r_dihedral_angle_3_deg 16.999 r_dihedral_angle_4_deg 15.796 r_dihedral_angle_1_deg 6.646 r_mcangle_it 3.858 r_mcbond_it 2.988 r_mcbond_other 2.984 r_angle_refined_deg 1.905 r_angle_other_deg 0.936 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.875 r_dihedral_angle_3_deg 16.999 r_dihedral_angle_4_deg 15.796 r_dihedral_angle_1_deg 6.646 r_mcangle_it 3.858 r_mcbond_it 2.988 r_mcbond_other 2.984 r_angle_refined_deg 1.905 r_angle_other_deg 0.936 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8520 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling