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Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component in the branched-chain alpha-ketoacid dehydrogenase complex (BCKDC), Oxidized Coenzyme A-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IHW PDB entry 2IHW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 292 0.1 M Na-acetate (pH 4.6), 28% PEG 4000, 0.15 M NH4-acetate, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.915 α = 90 b = 194.915 β = 90 c = 171.997 γ = 120
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 2005-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98000 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 2.17 50 97.8 0.048 13.2 3.1 126277
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 2.17 2.25 91.9 0.39 2.4 11855
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2IHW 2.17 50 123658 6243 95.71 0.205 0.202 0.2247 0.259 0.2709 RANDOM 39.03
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] -0.81 -0.4 -0.81 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.078 r_dihedral_angle_3_deg 17.851 r_dihedral_angle_4_deg 17.707 r_dihedral_angle_1_deg 6.74 r_scangle_it 3.751 r_scbond_it 2.585 r_angle_refined_deg 1.849 r_mcangle_it 1.576 r_mcbond_it 0.996 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.078 r_dihedral_angle_3_deg 17.851 r_dihedral_angle_4_deg 17.707 r_dihedral_angle_1_deg 6.74 r_scangle_it 3.751 r_scbond_it 2.585 r_angle_refined_deg 1.849 r_mcangle_it 1.576 r_mcbond_it 0.996 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.133 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14424 Nucleic Acid Atoms Solvent Atoms 742 Heterogen Atoms 439
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling