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Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design
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 6.5 2-7% POLYETHYLENE GLYCOL 3350, 5MM MGSO4 AND 50MM MES PH6.5, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.29 46.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.331 α = 90 b = 63.331 β = 90 c = 166.412 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU IMAGE PLATE 2005-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 3.1 30 94.8 0.15 8.5 3.8 13636 2.3
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 3.1 3.21 87.9 0.49 2.3 2.8
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 1W4R 3.1 30 12144 637 94.3 0.258 0.257 0.2542 0.289 0.2895 RANDOM 42.97
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] 3.69 1.84 3.69 -5.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.436 r_dihedral_angle_3_deg 17.464 r_dihedral_angle_4_deg 15.437 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 1.426 r_scangle_it 0.827 r_scbond_it 0.485 r_symmetry_vdw_refined 0.483 r_mcangle_it 0.327 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.436 r_dihedral_angle_3_deg 17.464 r_dihedral_angle_4_deg 15.437 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 1.426 r_scangle_it 0.827 r_scbond_it 0.485 r_symmetry_vdw_refined 0.483 r_mcangle_it 0.327 r_nbtor_refined 0.32 r_nbd_refined 0.27 r_mcbond_it 0.19 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other 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 5206 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing