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E. coli Pyruvate dehydrogenase E1 component E401K mutant with phosphonolactylthiamin diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IEA PDB ENTRY 2IEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.05 295 PEG 2000 monomethyl ether, proponal, sodium azide, hepes buffer, magnesium chloride, phosphonolactylthiamin diphosphate, pH 7.05, Vapour diffusion, temperature 295K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.61 α = 90 b = 142.11 β = 102.68 c = 82.14 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 2005-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
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 1.77 47.53 96.7 0.112 0.112 16.5 3.5 170761 160246 18.9
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) 1 1.77 1.83 89.4 0.415 0.415 2.5 2.8 15740
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 DIFFERENCE FOURIER THROUGHOUT PDB ENTRY 2IEA 1.77 47.53 170761 160246 8037 97.1 0.232 0.225 0.2245 0.255 0.2543 RANDOM 22.4
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] -1.55 0.64 -0.37 1.92
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_angle_deg 1.6 c_improper_angle_d 1.01 c_mcangle_it 0.416 c_scangle_it 0.325 c_mcbond_it 0.224 c_scbond_it 0.189 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12682 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 70
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling