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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 The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 1.83 32.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.673 α = 90 b = 232.294 β = 91.2 c = 91.936 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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.35 77 98.9 0.08 0.091 13.9 4.2 117919 3.1 3.1
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) 2.35 2.46 91.9 0.227 0.265 5.9 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 2.35 72.17 111973 111973 5906 98.9 0.19248 0.1896 0.1909 0.24718 0.2461 RANDOM 28.681
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] 2.25 0.25 -0.93 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.564 r_dihedral_angle_1_deg 23.503 r_dihedral_angle_4_deg 11.301 r_dihedral_angle_3_deg 10.493 r_mcangle_it 1.953 r_mcbond_it 1.686 r_angle_refined_deg 1.14 r_scangle_it 0.569 r_symmetry_hbond_refined 0.448 r_symmetry_vdw_refined 0.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.564 r_dihedral_angle_1_deg 23.503 r_dihedral_angle_4_deg 11.301 r_dihedral_angle_3_deg 10.493 r_mcangle_it 1.953 r_mcbond_it 1.686 r_angle_refined_deg 1.14 r_scangle_it 0.569 r_symmetry_hbond_refined 0.448 r_symmetry_vdw_refined 0.408 r_scbond_it 0.341 r_nbtor_refined 0.326 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.22 r_symmetry_metal_ion_refined 0.211 r_chiral_restr 0.17 r_metal_ion_refined 0.138 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_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 22043 Nucleic Acid Atoms Solvent Atoms 1127 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing