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Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 60-65% MPD + 0.1 M Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.16 α = 90 b = 59.31 β = 103.02 c = 61.3 γ = 90
Symmetry Space Group C 1 2 1
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 mirror 2005-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 28 95.6 0.065 13 4.1 57288 54800 -3 16.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.6 88.4 0.32 4.5 3.45 8115
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 28 49113 5515 95.56 0.17547 0.17085 0.171 0.21665 0.2157 RANDOM 22.028
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] -0.43 0.11 0.79 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.038 r_dihedral_angle_4_deg 15.998 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_1_deg 5.491 r_scangle_it 4.608 r_scbond_it 2.897 r_mcangle_it 1.79 r_angle_refined_deg 1.686 r_mcbond_it 1.096 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.038 r_dihedral_angle_4_deg 15.998 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_1_deg 5.491 r_scangle_it 4.608 r_scbond_it 2.897 r_mcangle_it 1.79 r_angle_refined_deg 1.686 r_mcbond_it 1.096 r_nbtor_refined 0.312 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.093 r_metal_ion_refined 0.047 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2659 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing