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Crystal structure of R145E mutant of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 295 0.2M Ammonium acetate, 0.1M HEPES, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.82 α = 97.01 b = 51.55 β = 105.9 c = 51.76 γ = 111.66
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 2016-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.21 48.2 91.2 0.062 0.997 15 3.9 17428 27.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.29 64.9 0.253 0.896 4.9 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PBR 2.23 48.2 16554 838 93.11 0.2312 0.22871 0.28113 0.2558 RANDOM 28.873
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] -1.1 -0.11 0.39 -0.34 0.68 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.713 r_dihedral_angle_4_deg 20.784 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 5.818 r_long_range_B_refined 3.002 r_long_range_B_other 3.002 r_scangle_other 1.782 r_mcangle_it 1.595 r_mcangle_other 1.595 r_angle_refined_deg 1.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.713 r_dihedral_angle_4_deg 20.784 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 5.818 r_long_range_B_refined 3.002 r_long_range_B_other 3.002 r_scangle_other 1.782 r_mcangle_it 1.595 r_mcangle_other 1.595 r_angle_refined_deg 1.206 r_scbond_it 1.038 r_scbond_other 1.037 r_mcbond_it 0.94 r_mcbond_other 0.937 r_angle_other_deg 0.887 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.003 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 3138 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing