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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 protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 1.86 33.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.247 α = 90 b = 231.995 β = 90.74 c = 92.614 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 MARMOSAIC 225 mm CCD mirror 2005-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9795 ESRF ID23-1
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 66 98.9 0.111 0.111 3.1 3.7 99540 99351 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 99.9 0.26 0.302 5.4 3.7
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 59.44 94324 94324 5027 98.86 0.19233 0.18848 0.1885 0.26303 0.2637 RANDOM 42.879
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] 2.23 0.06 -0.31 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.56 r_dihedral_angle_4_deg 17.147 r_dihedral_angle_3_deg 13.013 r_scangle_it 10.492 r_scbond_it 8.418 r_mcangle_it 5.28 r_mcbond_it 3.954 r_angle_refined_deg 1.282 r_dihedral_angle_1_deg 1.161 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.56 r_dihedral_angle_4_deg 17.147 r_dihedral_angle_3_deg 13.013 r_scangle_it 10.492 r_scbond_it 8.418 r_mcangle_it 5.28 r_mcbond_it 3.954 r_angle_refined_deg 1.282 r_dihedral_angle_1_deg 1.161 r_nbtor_refined 0.327 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.244 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.133 r_symmetry_hbond_refined 0.125 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 21953 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection MOSFLM data reduction SCALA data scaling AMoRE phasing