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Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W85 PDB entry 1w85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 1.82 32.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.312 α = 90 b = 232.82 β = 91.83 c = 92.004 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9793 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 85 87.5 0.098 0.11 11.6 4.8 110903 110687 2.6 2.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.64 79.3 0.41 0.48 2.9 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1w85 2.5 72.17 90276 90417 4664 96.21 0.17594 0.1726 0.1763 0.24052 0.1778 RANDOM 35.44
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] 2.6 -0.2 -0.3 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.135 r_dihedral_angle_4_deg 16.809 r_dihedral_angle_3_deg 12.371 r_scangle_it 11.449 r_scbond_it 9.043 r_mcangle_it 5.509 r_mcbond_it 3.978 r_angle_refined_deg 1.221 r_dihedral_angle_1_deg 1.135 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.135 r_dihedral_angle_4_deg 16.809 r_dihedral_angle_3_deg 12.371 r_scangle_it 11.449 r_scbond_it 9.043 r_mcangle_it 5.509 r_mcbond_it 3.978 r_angle_refined_deg 1.221 r_dihedral_angle_1_deg 1.135 r_nbtor_refined 0.33 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.255 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.088 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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_refined 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21519 Nucleic Acid Atoms Solvent Atoms 990 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing