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T18V 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 2.1 36.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.926 α = 90 b = 47.559 β = 90 c = 152.048 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 2016-05-27 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 1.73 50.01 90.8 22.7 6.6 33344
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 1.73 1.76
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 1.73 50.01 30435 1580 87.79 0.18053 0.17806 0.1919 0.22651 0.2345 RANDOM 20.563
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] -0.28 0.19 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.207 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 13.852 r_dihedral_angle_1_deg 5.754 r_long_range_B_refined 5.232 r_long_range_B_other 5.15 r_scangle_other 3.7 r_mcangle_it 2.659 r_mcangle_other 2.659 r_scbond_it 2.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.207 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 13.852 r_dihedral_angle_1_deg 5.754 r_long_range_B_refined 5.232 r_long_range_B_other 5.15 r_scangle_other 3.7 r_mcangle_it 2.659 r_mcangle_other 2.659 r_scbond_it 2.484 r_scbond_other 2.413 r_angle_refined_deg 1.968 r_mcbond_it 1.867 r_mcbond_other 1.867 r_angle_other_deg 1.065 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2851 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction SCALEPACK data scaling PHASER phasing