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Crystal structure of vaccinia virus thymidylate kinase bound to TDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E2G PDB ENTRY 1E2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 23% PEG 400, 100 MM NA ACETATE, 100 MM MES PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.75 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.77 α = 90 b = 55.59 β = 90 c = 161.17 γ = 90
Symmetry Space Group P 21 21 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.4 30 97.2 0.1 12.3 4 79520 -3 46
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 2.4 2.55 93.6 0.59 2.25 4
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 1E2G 2.4 30 20139 1024 97.4 0.2163 0.2163 0.2208 0.276 0.282 RANDOM 40.63
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] 0.569 10.451 -11.021
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.32742 c_bond_d 0.007289 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.32742 c_bond_d 0.007289 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3247 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 60
Software Software Software Name Purpose CNS refinement XDS data reduction XDS data scaling PHASER phasing