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V158T mutant of thermus thermophilus HB8 thymidylate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X7J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.1M Sodium Malonate, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.9 35.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.6 α = 90 b = 47.3 β = 90 c = 151.41 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 2016-05-18 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) R Merge I (Observed) CC (Half) 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 1.67 34.51 97.5 0.059 0.998 21 7.1 39094
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7
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 5X7J 1.67 34.51 37207 1834 98.13 0.17883 0.17753 0.1899 0.20581 0.2139 RANDOM 17.392
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] 0.4 -0.12 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.41 r_dihedral_angle_4_deg 19.328 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_1_deg 5.528 r_long_range_B_refined 4.89 r_long_range_B_other 4.872 r_scangle_other 3.391 r_mcangle_it 2.478 r_mcangle_other 2.478 r_scbond_it 2.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.41 r_dihedral_angle_4_deg 19.328 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_1_deg 5.528 r_long_range_B_refined 4.89 r_long_range_B_other 4.872 r_scangle_other 3.391 r_mcangle_it 2.478 r_mcangle_other 2.478 r_scbond_it 2.173 r_scbond_other 2.173 r_angle_refined_deg 1.853 r_mcbond_it 1.607 r_mcbond_other 1.603 r_angle_other_deg 1.029 r_chiral_restr 0.103 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 2854 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling PHASER phasing