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The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 LITHIUM SULPHATE, HEPES, DTT, DT, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.53 51.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.4 α = 90 b = 117.5 β = 90 c = 108.6 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 AREA DETECTOR MULTIWIRE SIEMENS 1998-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 2.5 20 92 0.063 0.063 11.5 2.4 23273 28.3
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) 1 2.5 2.64 92 0.17 0.17 3.1 1.6
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VTK 2.5 20 23273 1164 91 0.212 0.2077 0.273 0.2606 RANDOM 28.4
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]
RMS Deviations Key Refinement Restraint Deviation p_angle_d 0.022 p_bond_d 0.009 p_angle_deg p_planar_d p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_plane_restr
RMS Deviations Key Refinement Restraint Deviation p_angle_d 0.022 p_bond_d 0.009 p_angle_deg p_planar_d p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_plane_restr p_chiral_restr p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4729 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling AMoRE phasing