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Crystal structure of human thiamin pyrophosphokinase 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 25% peg-3350, 0.2M ammonium sulfate, 0.1M sodium cacodylate. 0.02M ATP, 0.004M magnesium chloride were added to the protein stock solution, pH 5.5, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.7 α = 90 b = 97.39 β = 113.08 c = 63.65 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS 2011-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 1.8 29.587 99.8 0.042 45.23 48623 -3 29.513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 99.9 0.479 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 29.587 48583 2100 99.895 0.174 0.1723 0.2034 0.2032 THIN SHELLS (SFTOOLS) 18.995
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] -0.662 -0.976 -0.221 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.31 r_dihedral_angle_4_deg 12.821 r_dihedral_angle_3_deg 11.381 r_dihedral_angle_1_deg 5.788 r_scangle_it 2.842 r_scbond_it 1.762 r_angle_refined_deg 1.292 r_mcangle_it 1.137 r_angle_other_deg 0.869 r_mcbond_it 0.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.31 r_dihedral_angle_4_deg 12.821 r_dihedral_angle_3_deg 11.381 r_dihedral_angle_1_deg 5.788 r_scangle_it 2.842 r_scbond_it 1.762 r_angle_refined_deg 1.292 r_mcangle_it 1.137 r_angle_other_deg 0.869 r_mcbond_it 0.629 r_mcbond_other 0.14 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3495 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 88
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction