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Y162F 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 Magnesium formate dehydrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.87 34.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.1 α = 90 b = 47.1 β = 90 c = 151.26 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 2016-05-16 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 1.76 37.81 100 0.099 0.994 11.3 7.6 33617 17.35
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 1.76 1.79
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 1.76 37.81 31900 1648 99.93 0.18322 0.18086 0.1898 0.22785 0.2313 RANDOM 23.742
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] 1.03 -0.62 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.488 r_dihedral_angle_4_deg 19.759 r_dihedral_angle_3_deg 13.802 r_dihedral_angle_1_deg 5.326 r_long_range_B_refined 4.619 r_long_range_B_other 4.499 r_scangle_other 2.261 r_angle_refined_deg 1.981 r_mcangle_it 1.755 r_mcangle_other 1.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.488 r_dihedral_angle_4_deg 19.759 r_dihedral_angle_3_deg 13.802 r_dihedral_angle_1_deg 5.326 r_long_range_B_refined 4.619 r_long_range_B_other 4.499 r_scangle_other 2.261 r_angle_refined_deg 1.981 r_mcangle_it 1.755 r_mcangle_other 1.755 r_scbond_it 1.404 r_scbond_other 1.382 r_angle_other_deg 1.08 r_mcbond_it 1.058 r_mcbond_other 1.057 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 2879 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing