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Complex between the human thiamine triphosphatase and 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 VAPOR DIFFUSION, HANGING DROP 4.2 293 O.1 citrate, 0.2 Ammonium sulfate, triphosphate 0.1M, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.93 36.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.378 α = 90 b = 63.529 β = 108.75 c = 70.95 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 2010-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9797 ESRF BM30A
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 2.3 46.2 94.8 0.099 9 3.2 16547 16547
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 2.3 2.42 78.2 0.45 2.6 3.1 1979
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 MIR THROUGHOUT PDB entry 3BHD 2.3 46.16 15702 15702 832 94.5 0.18429 0.18429 0.18038 0.1817 0.26085 0.2604 RANDOM 28.326
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] -0.17 0.44 0.92 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.389 r_dihedral_angle_4_deg 17.373 r_dihedral_angle_3_deg 16.843 r_dihedral_angle_1_deg 6.37 r_scangle_it 4.845 r_mcangle_it 3.745 r_scbond_it 3.173 r_mcbond_it 2.3 r_angle_refined_deg 1.574 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.389 r_dihedral_angle_4_deg 17.373 r_dihedral_angle_3_deg 16.843 r_dihedral_angle_1_deg 6.37 r_scangle_it 4.845 r_mcangle_it 3.745 r_scbond_it 3.173 r_mcbond_it 2.3 r_angle_refined_deg 1.574 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3160 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 38
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement XDS data reduction SCALA data scaling