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Y92H mutant of thermus thermophilus HB8 thymidylate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.1M Sodium Malonate, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.89 34.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.54 α = 90 b = 47.052 β = 90 c = 151.48 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 IMAGE PLATE MAR scanner 345 mm plate 2016-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.542
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 1.66 50.01 97.8 20.7 7 39038
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.66 50.01 37150 1820 97.45 0.1728 0.17158 0.19836 0.2206 RANDOM 25.279
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] 0.24 -0.09 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.173 r_dihedral_angle_4_deg 19.641 r_dihedral_angle_3_deg 13.137 r_dihedral_angle_1_deg 5.631 r_long_range_B_refined 5.313 r_long_range_B_other 5.269 r_scangle_other 4.059 r_mcangle_other 2.943 r_mcangle_it 2.941 r_scbond_it 2.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.173 r_dihedral_angle_4_deg 19.641 r_dihedral_angle_3_deg 13.137 r_dihedral_angle_1_deg 5.631 r_long_range_B_refined 5.313 r_long_range_B_other 5.269 r_scangle_other 4.059 r_mcangle_other 2.943 r_mcangle_it 2.941 r_scbond_it 2.747 r_scbond_other 2.746 r_mcbond_it 2.011 r_mcbond_other 2.003 r_angle_refined_deg 1.872 r_angle_other_deg 1.053 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2847 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing