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Thymidine kinase from B. anthracis in complex with dT.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XMR PDP ENTRY 1XMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 5% 1,2-PROPANEDIOL 0.1M NA/K PHOSPHATE PH 6 10% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.1 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.171 α = 90 b = 73.171 β = 90 c = 223.734 γ = 90
Symmetry Space Group I 41 2 2
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 ID14-2 ESRF ID14-2
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 2.7 25.87 99.9 0.11 22.6 14.1 8799 2
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 2.7 2.85 100 0.49 5.9 14.5
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 PDP ENTRY 1XMR 2.7 25.87 8366 415 100 0.205 0.203 0.2024 0.244 0.2435 RANDOM 42.79
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] 2.51 2.51 -5.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.099 r_dihedral_angle_3_deg 17.524 r_dihedral_angle_4_deg 16.842 r_dihedral_angle_1_deg 5.927 r_scangle_it 1.88 r_angle_refined_deg 1.343 r_scbond_it 1.132 r_mcangle_it 0.841 r_mcbond_it 0.456 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.099 r_dihedral_angle_3_deg 17.524 r_dihedral_angle_4_deg 16.842 r_dihedral_angle_1_deg 5.927 r_scangle_it 1.88 r_angle_refined_deg 1.343 r_scbond_it 1.132 r_mcangle_it 0.841 r_mcbond_it 0.456 r_nbtor_refined 0.308 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.212 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.089 r_bond_refined_d 0.011 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 1385 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing