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Crystal Structure of Human Thymidine Kinase 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 288 sodium citrate, 2-propanol, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K
Crystal Properties Matthews coefficient Solvent content 3 58.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.672 α = 90 b = 123.177 β = 130.2 c = 116 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 ADSC QUANTUM 4 2003-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.25 87.7 28.4 0.101 4.9 3.5 77566 77566 1 1
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) 2.25 2.37 98.6 0.434 1.5 3.5 11361
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 SIRAS THROUGHOUT 2.4 42.07 62088 3317 98.92 0.20288 0.20133 0.2007 0.23204 0.2299 RANDOM 34.695
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] 2.86 1.78 -0.5 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.619 r_scangle_it 2.541 r_scbond_it 1.461 r_angle_refined_deg 1.259 r_mcangle_it 1.024 r_mcbond_it 0.519 r_metal_ion_refined 0.235 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.619 r_scangle_it 2.541 r_scbond_it 1.461 r_angle_refined_deg 1.259 r_mcangle_it 1.024 r_mcbond_it 0.519 r_metal_ion_refined 0.235 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9990 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 248
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling autoSHARP phasing