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E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin Diphosphate Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L8A PDB ENTRY 1L8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, PHOSPHONOLACTYL- THIAMIN DIPHOSPHATE, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.34 47.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.57 α = 90 b = 142.51 β = 102.37 c = 82.09 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 93 AREA DETECTOR SIEMENS HI-STAR Osmic Mirrors 2002-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.1 40.5 94 0.065 0.087 24.82 4.7 99699 99699
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.19 60 5.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1L8A 2.1 8 2 99699 95052 4807 94 0.204 0.185 0.185 0.1804 0.244 0.2336 RANDOM 10.55
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.87 x_scangle_it 3.129 x_scbond_it 2.166 x_mcangle_it 1.698 x_angle_deg 1.3 x_mcbond_it 1.11 x_improper_angle_d 0.72 x_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13182 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 95
Software Software Software Name Purpose X-GEN data scaling FBSCALE data reduction PHASES phasing X-PLOR refinement FRAMBO data collection FBSCALE data scaling