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Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Morpheus screen c6: 10% PEG 8000, 20% EG; 30mM each NaNO3, Na2HPO4, (NH4)2SO4; 100mM MOPS/HEPES pH 7.5; ButhA.0010.l.B1.PS01726 at 10mg/ml with 2.5mM NAD; direct cryo; tray 252631c6, puck sxz2-6
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.22 α = 103.26 b = 77.1 β = 93.98 c = 109.35 γ = 109.68
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 RAYONIX MX-225 2014-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.65 50 97.1 0.081 0.094 11.23 4 253404 246070 -3 22.006
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 95.4 0.476 0.55 2.88 4
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 3TPC 1.65 50 233814 12256 97.15 0.1557 0.1545 0.1691 0.1771 0.1887 RANDOM 16.931
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] 0.29 -0.56 0.22 -0.19 -0.01 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.291 r_dihedral_angle_4_deg 17.08 r_dihedral_angle_3_deg 11.797 r_dihedral_angle_1_deg 5.993 r_angle_refined_deg 1.74 r_mcangle_it 1.107 r_angle_other_deg 0.98 r_mcbond_it 0.634 r_mcbond_other 0.633 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.291 r_dihedral_angle_4_deg 17.08 r_dihedral_angle_3_deg 11.797 r_dihedral_angle_1_deg 5.993 r_angle_refined_deg 1.74 r_mcangle_it 1.107 r_angle_other_deg 0.98 r_mcbond_it 0.634 r_mcbond_other 0.633 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14506 Nucleic Acid Atoms Solvent Atoms 1923 Heterogen Atoms 468
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing ARP model building Coot model building REFMAC refinement PDB_EXTRACT data extraction