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Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XMR PDB ENTRY 1XMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 287 15% PEG3350, 0.3 M Ammonium formate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.05 40.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.158 α = 90 b = 115.649 β = 101.02 c = 64.474 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 MARRESEARCH Toroidal mirror 2005-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 26.95 99.1 0.082 0.082 16.4 5 54540 54484 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 0.424 0.424 1.8 4.3
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 (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 1XMR 2 26.95 54456 51687 2769 98.96 0.19741 0.19535 0.2097 0.235 0.2413 RANDOM 32.885
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] -0.94 -0.16 1.83 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.991 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_4_deg 12.463 r_dihedral_angle_1_deg 5.178 r_scangle_it 1.395 r_angle_refined_deg 1.04 r_scbond_it 0.912 r_mcangle_it 0.631 r_mcbond_it 0.367 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.991 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_4_deg 12.463 r_dihedral_angle_1_deg 5.178 r_scangle_it 1.395 r_angle_refined_deg 1.04 r_scbond_it 0.912 r_mcangle_it 0.631 r_mcbond_it 0.367 r_nbtor_refined 0.301 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_refined 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 6380 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 80
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ProDC data collection CCP4 data scaling