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Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 12% PEG 8000, 140mM NaOAC, 50mM BisTris pH6.5, 10% glucose, 50mM Taurine, 8mM MgCl2, and 10mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.92 57.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.389 α = 90 b = 129.668 β = 109.15 c = 144.946 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 QUANTUM 315 2008-02-15 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 2.998 50 99.8 0.146 10.699 3.7 72201
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 2.998 3.05 98.2 0.56 3.4 3543
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 2.998 50 72121 3624 99.37 0.189 0.185 0.1901 0.263 0.2659 RANDOM 21.411
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] 0.09 1.8 -3.18 4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.919 r_dihedral_angle_3_deg 21.975 r_dihedral_angle_4_deg 20.649 r_dihedral_angle_1_deg 7.307 r_scangle_it 3.883 r_scbond_it 2.287 r_angle_refined_deg 2.025 r_mcangle_it 1.342 r_mcbond_it 0.664 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.919 r_dihedral_angle_3_deg 21.975 r_dihedral_angle_4_deg 20.649 r_dihedral_angle_1_deg 7.307 r_scangle_it 3.883 r_scbond_it 2.287 r_angle_refined_deg 2.025 r_mcangle_it 1.342 r_mcbond_it 0.664 r_chiral_restr 0.122 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21386 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 112
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction