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Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase from Ralstonia eutropha in complexed with acetoacetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 ethanol, citrate, lithium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.92 57.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.57 α = 90 b = 139.57 β = 90 c = 70.621 γ = 90
Symmetry Space Group P 4 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 270 2013-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97949 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 1.34 50 99.4 0.067 56.5 16.1 151127
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 1.34 1.37 99 0.295 5.6 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1q7b 1.34 23.39 146641 7752 99.35 0.1691 0.1681 0.1699 0.1878 0.1891 RANDOM 19.4431
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] 0.57 0.57 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.157 r_dihedral_angle_4_deg 20.642 r_dihedral_angle_3_deg 11.723 r_dihedral_angle_1_deg 5.748 r_mcangle_it 2.973 r_angle_refined_deg 2.446 r_mcbond_it 2.013 r_mcbond_other 2.004 r_angle_other_deg 1.048 r_chiral_restr 0.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.157 r_dihedral_angle_4_deg 20.642 r_dihedral_angle_3_deg 11.723 r_dihedral_angle_1_deg 5.748 r_mcangle_it 2.973 r_angle_refined_deg 2.446 r_mcbond_it 2.013 r_mcbond_other 2.004 r_angle_other_deg 1.048 r_chiral_restr 0.175 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3702 Nucleic Acid Atoms Solvent Atoms 543 Heterogen Atoms 144
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling