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The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QS0 PDB ENTRY 1QS0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00
Crystal Properties Matthews coefficient Solvent content 2.21 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.27 α = 90 b = 232.33 β = 90.81 c = 91.924 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 CCD 2003-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 20 94.6 0.07 13.8 3 171898
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 2.07 68.4 0.26 2.7
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QS0 2 20 171898 9031 94.8 0.178 0.176 0.1767 0.215 0.215 RANDOM 21.98
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] 1.86 -0.32 -0.46 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.773 r_dihedral_angle_4_deg 18.551 r_dihedral_angle_3_deg 15.833 r_dihedral_angle_1_deg 5.532 r_angle_refined_deg 1.352 r_mcangle_it 0.645 r_scangle_it 0.587 r_mcbond_it 0.408 r_scbond_it 0.393 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.773 r_dihedral_angle_4_deg 18.551 r_dihedral_angle_3_deg 15.833 r_dihedral_angle_1_deg 5.532 r_angle_refined_deg 1.352 r_mcangle_it 0.645 r_scangle_it 0.587 r_mcbond_it 0.408 r_scbond_it 0.393 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.206 r_chiral_restr 0.138 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.125 r_metal_ion_refined 0.074 r_bond_refined_d 0.014 r_gen_planes_refined 0.001 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_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21642 Nucleic Acid Atoms Solvent Atoms 1733 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing