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Mouse Thiamin Pyrophosphokinase in a Ternary Complex with Pyrithiamin Pyrophosphate and AMP at 2.5 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IG3 PDB ENTRY 1IG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 298 Crystallization experiments were set up by incubating mouse TPK with pyrithiamin and MgATP prior to adding the equilibrium mixture of enzyme, substrate and products to the previously determined crystallization conditions. , pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.363 α = 90 b = 89.363 β = 90 c = 141.43 γ = 120
Symmetry Space Group P 31 2 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 2004-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0000 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 94.5 0.117 8.94 3.98 23271 21991 0.2 62.382
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 96.7 0.614 2.12 2.8 2271
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IG3 2.5 50 23271 21991 1085 94.5 0.26 0.24 0.237 0.2371 0.252 0.2528 Random
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 c_dihedral_angle_d 24.6627 c_angle_deg 1.318 c_improper_angle_d 0.9793 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3897 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 124
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling CNS refinement HKL-2000 data reduction CNS phasing