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Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 293 PEG4000, pH 5.80, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.672 α = 90 b = 145.672 β = 90 c = 69.236 γ = 120
Symmetry Space Group P 31 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 315 2002-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 1.73 50 98.9 0.068 25.2 86997 -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 1.73 1.76 98 0.667
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 (All) 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 1OLS 1.73 50 85528 1469 98.84 0.14777 0.14777 0.1472 0.182 0.18083 0.2058 RANDOM 21.178
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] 0.78 0.39 0.78 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 18.877 r_dihedral_angle_3_deg 13.728 r_dihedral_angle_1_deg 5.752 r_scangle_it 4.715 r_scbond_it 3 r_angle_refined_deg 1.703 r_mcangle_it 1.677 r_mcbond_it 0.986 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.851 r_dihedral_angle_4_deg 18.877 r_dihedral_angle_3_deg 13.728 r_dihedral_angle_1_deg 5.752 r_scangle_it 4.715 r_scbond_it 3 r_angle_refined_deg 1.703 r_mcangle_it 1.677 r_mcbond_it 0.986 r_nbtor_refined 0.313 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.201 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.138 r_metal_ion_refined 0.108 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5514 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction AMoRE phasing REFMAC refinement HKL-2000 data scaling