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E. Coli Pyruvate Dehydrogenase H407A variant Phosphonolactylthiamin Diphosphate Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.05 291 PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, PHOSPHONOLACTYL- THIAMIN DIPHOSPHATE, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K, pH 7.05
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.99 α = 90 b = 143.2 β = 102.61 c = 82.53 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 2004-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00013 APS 22-ID
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 1.55 41.77 79.4 0.076 12.26 3.2 237104 213020 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.55 1.67 32.8 1.46
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 (All) 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 DIFFERENCE FOURIER THROUGHOUT 1L8A 1.85 41.77 157076 150327 7535 95.2 0.227 0.216 0.216 0.2156 0.24 0.24 RANDOM 21.1
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] -1.81 0.48 0.79 1.02
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_angle_deg 1.5 c_improper_angle_d 0.94 c_mcangle_it 0.469 c_scangle_it 0.411 c_mcbond_it 0.255 c_scbond_it 0.246 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12682 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 70
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling PHASES phasing CNS refinement HKL-2000 data reduction