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catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W4R PDB ENTRY 1W4R
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 = 114.68 α = 90 b = 114.68 β = 90 c = 105.6 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 I04 Diamond I04
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 44.25 99.9 0.08 17 14.3 31864 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 2.3 2.39 99.9 1.02 2.6 14.3
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 1W4R 2.3 114.68 30146 1708 99.81 0.18016 0.17869 0.1867 0.20745 0.191 RANDOM 58.235
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] -0.77 -0.77 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.236 r_dihedral_angle_4_deg 15.695 r_dihedral_angle_3_deg 13.088 r_mcangle_it 8.032 r_scbond_it 7.735 r_dihedral_angle_1_deg 6.603 r_mcbond_it 5.985 r_mcbond_other 5.979 r_angle_refined_deg 2.217 r_angle_other_deg 1.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.236 r_dihedral_angle_4_deg 15.695 r_dihedral_angle_3_deg 13.088 r_mcangle_it 8.032 r_scbond_it 7.735 r_dihedral_angle_1_deg 6.603 r_mcbond_it 5.985 r_mcbond_other 5.979 r_angle_refined_deg 2.217 r_angle_other_deg 1.573 r_chiral_restr 0.123 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.009 r_gen_planes_other 0.007 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 2588 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing