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Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex with the subunit-binding domain (SBD) of E2p, but SBD cannot be modeled into the electron density
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 Mix the proteins with the ratio of E1p:SBD=1:2.10% PEG 6000, 1.5M NaCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.63 66.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.378 α = 90 b = 154.378 β = 90 c = 82.949 γ = 120
Symmetry Space Group P 32 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 2005-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98 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 2.2 50 99.5 0.034 33 6.6 57582
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 2.24 95.5 0.558 2 6.5 2736
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.2 50 56609 1511 97.78 0.189 0.187 0.1877 0.226 0.2242 RANDOM 49.348
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] -2.85 -1.42 -2.85 4.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.689 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_4_deg 14.452 r_dihedral_angle_1_deg 6.356 r_scangle_it 4.695 r_scbond_it 2.98 r_angle_refined_deg 1.733 r_mcangle_it 1.588 r_mcbond_it 0.882 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.689 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_4_deg 14.452 r_dihedral_angle_1_deg 6.356 r_scangle_it 4.695 r_scbond_it 2.98 r_angle_refined_deg 1.733 r_mcangle_it 1.588 r_mcbond_it 0.882 r_chiral_restr 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5098 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling