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Crystal structure of EHV4-TK complexed with Thy and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VTK PDB entry 1VTK with unconserved residues modified to alanine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 Ammonium sulfate, MES, Dioxane , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.301 α = 90 b = 121.014 β = 90 c = 118.808 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 47461
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 (All) 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 1VTK with unconserved residues modified to alanine 2.1 29.7 41415 41415 4541 96.78 0.18886 0.18886 0.18418 0.1901 0.23175 0.1878 RANDOM 28.256
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] 1.48 -0.42 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.453 r_scangle_it 3.04 r_scbond_it 1.953 r_angle_refined_deg 1.343 r_mcangle_it 1.329 r_mcbond_it 0.718 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.453 r_scangle_it 3.04 r_scbond_it 1.953 r_angle_refined_deg 1.343 r_mcangle_it 1.329 r_mcbond_it 0.718 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5009 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement DENZO data reduction XSCALE data scaling MOLREP phasing