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Crystal structure of 3-hydroxybutylryl-CoA dehydrogenase with NAD from 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 (NH4)2SO4, CAPs, Li2SO4, pH 10.5, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.51 64.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.45 α = 90 b = 148.45 β = 90 c = 201.63 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 2010-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97985 PAL/PLS 7A (6B, 6C1)
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 2.3 50 89.5 0.066 17.4 3.7 73562 65804
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 2.3 2.38 89.6 0.296 3.1 6596
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 2.3 43.81 62472 65803 3331 89.41 0.2214 0.2182 0.223 0.2815 0.2846 RANDOM 53.429
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] 0.67 0.67 0.67 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.595 r_dihedral_angle_3_deg 18.154 r_dihedral_angle_4_deg 15.38 r_dihedral_angle_1_deg 7.015 r_mcangle_it 5.554 r_mcbond_it 4.1 r_mcbond_other 4.1 r_angle_refined_deg 1.83 r_angle_other_deg 0.847 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.595 r_dihedral_angle_3_deg 18.154 r_dihedral_angle_4_deg 15.38 r_dihedral_angle_1_deg 7.015 r_mcangle_it 5.554 r_mcbond_it 4.1 r_mcbond_other 4.1 r_angle_refined_deg 1.83 r_angle_other_deg 0.847 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8516 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 176
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction