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Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 2M (NH4)2SO4, 0.1M Cacodylate pH 6.5, 0.2M Sodium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.83 56.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.427 α = 90 b = 135.427 β = 90 c = 97.166 γ = 120
Symmetry Space Group P 32 2 1
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 2012-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.00 PAL/PLS 5C (4A)
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 2.6 50 96.8 30900
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 2.6 2.69 95.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.6 50 30900 29327 1564 96.79 0.21402 0.21105 0.2144 0.27131 0.2687 RANDOM 60.89
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] 2.22 1.11 2.22 -7.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.068 r_dihedral_angle_4_deg 19.113 r_dihedral_angle_3_deg 18.615 r_long_range_B_refined 9.304 r_long_range_B_other 9.304 r_dihedral_angle_1_deg 7.201 r_mcangle_it 6.125 r_mcangle_other 6.124 r_scangle_other 5.815 r_mcbond_other 3.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.068 r_dihedral_angle_4_deg 19.113 r_dihedral_angle_3_deg 18.615 r_long_range_B_refined 9.304 r_long_range_B_other 9.304 r_dihedral_angle_1_deg 7.201 r_mcangle_it 6.125 r_mcangle_other 6.124 r_scangle_other 5.815 r_mcbond_other 3.945 r_mcbond_it 3.944 r_scbond_it 3.68 r_scbond_other 3.679 r_angle_refined_deg 1.576 r_angle_other_deg 0.816 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6306 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling