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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 2.76 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 257.064 α = 90 b = 115.612 β = 113.64 c = 127.592 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV 2008-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
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 2.444 50 98.1 0.155 14.158 6.7 123888
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 2.444 2.49 96.6 0.693 6.5 6036
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 2.444 50 123754 6182 97.77 0.167 0.165 0.1657 0.211 0.21 RANDOM 18.89
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] 0.8 -0.25 0.62 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.808 r_dihedral_angle_3_deg 18.592 r_dihedral_angle_4_deg 17.687 r_dihedral_angle_1_deg 6.187 r_scangle_it 4.637 r_scbond_it 2.917 r_angle_refined_deg 1.842 r_mcangle_it 1.548 r_mcbond_it 0.806 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.808 r_dihedral_angle_3_deg 18.592 r_dihedral_angle_4_deg 17.687 r_dihedral_angle_1_deg 6.187 r_scangle_it 4.637 r_scbond_it 2.917 r_angle_refined_deg 1.842 r_mcangle_it 1.548 r_mcbond_it 0.806 r_chiral_restr 0.115 r_bond_refined_d 0.02 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21101 Nucleic Acid Atoms Solvent Atoms 792 Heterogen Atoms 142
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction