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Crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DM3 PDB ENTRY 1DM3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.6 100 MM MES PH 6.6, 15% MME-PEG5000
Crystal Properties Matthews coefficient Solvent content 2.36 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.73 α = 90 b = 196.77 β = 103.78 c = 79.65 γ = 90
Symmetry Space Group P 1 21 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 CCD TORROIDAL MIRROR 2011-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 48.17 99.6 0.07 15.07 3.7 109515 3
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 2.1 99.8 0.41 3.07 3.7
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 PDB ENTRY 1DM3 2 48.17 104049 5461 99.65 0.19695 0.19527 0.1811 0.22889 0.2099 RANDOM 24.104
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] -0.58 -0.81 -0.28 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.226 r_dihedral_angle_4_deg 14.233 r_dihedral_angle_3_deg 11.998 r_dihedral_angle_1_deg 5.88 r_mcangle_it 3.304 r_mcbond_it 2.253 r_angle_refined_deg 1.509 r_angle_other_deg 1.191 r_mcbond_other 0.611 r_symmetry_vdw_refined 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.226 r_dihedral_angle_4_deg 14.233 r_dihedral_angle_3_deg 11.998 r_dihedral_angle_1_deg 5.88 r_mcangle_it 3.304 r_mcbond_it 2.253 r_angle_refined_deg 1.509 r_angle_other_deg 1.191 r_mcbond_other 0.611 r_symmetry_vdw_refined 0.26 r_symmetry_hbond_refined 0.228 r_nbd_refined 0.227 r_symmetry_vdw_other 0.223 r_nbd_other 0.178 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.093 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.045 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.007 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11712 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing