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Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with Me-ARA-EdU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F0T PDB entry 3F0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 0.9-1.2M LI2SO4, 1MM DTT, 0.1M HEPES, PH 7.5-8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.5 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.42 α = 90 b = 116.83 β = 90 c = 108.31 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 CCD MARMOSAIC 225 mm CCD 2011-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 34.9 96.8 0.115 0.106 12.2 6.4 24367 24367 2 2 31.19
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 93.9 0.471 0.434 3.3 5.8 3413
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3F0T 2.5 34.871 1.34 24344 24330 1216 96.4 0.19 0.1867 0.1901 0.2505 0.2534 random 21.33
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 f_dihedral_angle_d 14.093 f_angle_d 1.207 f_chiral_restr 0.077 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 63
Software Software Software Name Purpose PHASER phasing PHENIX refinement MOSFLM data reduction SCALA data scaling