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D90L 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 0.2M MgCl2.6H2O, 0.1 M Tris hydrochloride, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.1 36.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.8 α = 90 b = 47.32 β = 90 c = 153.04 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 RIGAKU RAXIS IV 2016-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
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 2.26 76.64 91.9 9.3 7.9 15291
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 2.26 2.33
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 2.26 76.64 15242 721 91.55 0.2203 0.2181 0.2233 0.2629 0.2604 RANDOM 21.8676
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] -0.43 -0.3 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.874 r_dihedral_angle_4_deg 19.562 r_dihedral_angle_3_deg 16.15 r_dihedral_angle_1_deg 5.286 r_angle_other_deg 3.616 r_mcangle_it 1.678 r_angle_refined_deg 1.292 r_mcbond_it 0.913 r_mcbond_other 0.912 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.874 r_dihedral_angle_4_deg 19.562 r_dihedral_angle_3_deg 16.15 r_dihedral_angle_1_deg 5.286 r_angle_other_deg 3.616 r_mcangle_it 1.678 r_angle_refined_deg 1.292 r_mcbond_it 0.913 r_mcbond_other 0.912 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2844 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 25
Software Software Software Name Purpose PDB_EXTRACT data extraction REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing