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Crystal structure of mouse thiamine triphosphatase in complex with thiamine triphosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BHD PDB ENTRY 3BHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 1.6 M NA/K PHOSPHATE PH 6.8
Crystal Properties Matthews coefficient Solvent content 3.49 64.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.181 α = 90 b = 93.578 β = 93.04 c = 70.775 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 PIXEL DECTRIS PILATUS 6M 2013-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.1 70.68 99.5 0.06 19.34 4.58 39110 -3
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 2.1 2.23 98.3 0.58 2.36 4.49
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3BHD 2.1 70.68 37148 1963 99.53 0.21232 0.21125 0.2163 0.23199 0.2328 RANDOM 52.162
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] -1.12 1.2 -0.48 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.384 r_dihedral_angle_4_deg 16.319 r_dihedral_angle_3_deg 14.301 r_dihedral_angle_1_deg 6.063 r_angle_refined_deg 1.518 r_mcangle_it 1.292 r_scbond_it 1.006 r_angle_other_deg 0.933 r_mcbond_it 0.726 r_mcbond_other 0.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.384 r_dihedral_angle_4_deg 16.319 r_dihedral_angle_3_deg 14.301 r_dihedral_angle_1_deg 6.063 r_angle_refined_deg 1.518 r_mcangle_it 1.292 r_scbond_it 1.006 r_angle_other_deg 0.933 r_mcbond_it 0.726 r_mcbond_other 0.726 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3000 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing