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catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP or dThd
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FUV PDB ENTRY 5FUV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.1 M HEPES PH 7.0, 0.8 M SUCCINIC ACID 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2
Crystal Properties Matthews coefficient Solvent content 3.77 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.999 α = 90 b = 114.999 β = 90 c = 104.77 γ = 90
Symmetry Space Group P 43 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.2 64.24 100 0.1 11.8 11.6 36299 2
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 2.2 2.27 100 0.88 2.6 10.8
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 5FUV 2.2 115 34470 1757 99.88 0.1861 0.18532 0.194 0.20126 0.202 RANDOM 55.707
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] -1.23 -1.23 2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.005 r_dihedral_angle_3_deg 12.572 r_long_range_B_refined 12.472 r_long_range_B_other 12.472 r_dihedral_angle_4_deg 11.105 r_scangle_other 10.463 r_mcangle_it 7.817 r_mcangle_other 7.815 r_scbond_it 7.574 r_scbond_other 7.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.005 r_dihedral_angle_3_deg 12.572 r_long_range_B_refined 12.472 r_long_range_B_other 12.472 r_dihedral_angle_4_deg 11.105 r_scangle_other 10.463 r_mcangle_it 7.817 r_mcangle_other 7.815 r_scbond_it 7.574 r_scbond_other 7.409 r_dihedral_angle_1_deg 6.675 r_mcbond_it 5.71 r_mcbond_other 5.706 r_angle_refined_deg 2.16 r_angle_other_deg 1.636 r_chiral_restr 0.125 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_bond_other_d 0.009 r_gen_planes_other 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2577 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing