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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 2.1 50 97.5 0.095 14.3 48283 -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 2.1 2.14 71.8 0.386
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 2.1 50 46720 1542 97.4 0.14944 0.14944 0.14811 0.1832 0.18956 0.2143 RANDOM 23.527
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] 0.53 0.27 0.53 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.044 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 14.883 r_dihedral_angle_1_deg 6.136 r_scangle_it 4.611 r_scbond_it 2.96 r_angle_refined_deg 1.623 r_mcangle_it 1.6 r_mcbond_it 0.887 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.044 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 14.883 r_dihedral_angle_1_deg 6.136 r_scangle_it 4.611 r_scbond_it 2.96 r_angle_refined_deg 1.623 r_mcangle_it 1.6 r_mcbond_it 0.887 r_nbtor_refined 0.307 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.159 r_metal_ion_refined 0.123 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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 5519 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction AMoRE phasing REFMAC refinement HKL-2000 data scaling