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Crystal structure of human thiamine triphosphatase (THTPA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.8 300 50mM Citric acid, 0.2M Ammonium sulfate, 3mM Sodium tungstenate, 10mg/ml Protein, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 1.793 31.396
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.77 α = 90 b = 46.81 β = 113.97 c = 71.87 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 ADSC QUANTUM 315 2007-09-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.97915 ESRF ID14-2
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 1.5 20 99.6 0.061 13.79 3.51 115663 -3 20.28
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 1.5 1.6 99.7 0.421 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.5 19.96 59035 59035 2983 99.5 0.17774 0.17648 0.176 0.20117 0.1996 RANDOM 15.948
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] -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.093 r_dihedral_angle_4_deg 20.614 r_dihedral_angle_3_deg 13.269 r_dihedral_angle_1_deg 6.567 r_scangle_it 4.217 r_scbond_it 2.691 r_mcangle_it 1.639 r_angle_refined_deg 1.605 r_mcbond_it 0.94 r_metal_ion_refined 0.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.093 r_dihedral_angle_4_deg 20.614 r_dihedral_angle_3_deg 13.269 r_dihedral_angle_1_deg 6.567 r_scangle_it 4.217 r_scbond_it 2.691 r_mcangle_it 1.639 r_angle_refined_deg 1.605 r_mcbond_it 0.94 r_metal_ion_refined 0.884 r_nbtor_refined 0.309 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.209 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3261 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 77
Software Software Software Name Purpose XSCALE data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction ProDC data collection SHELXD phasing