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Crystal structure of Thymidylate kinase with TMP and its low-resolution (SAXS) solution structure from Brugia malayi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 300 Diammonium tartrate, Bis-Tris pH 6.0
Crystal Properties Matthews coefficient Solvent content 1.81 32.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.67 α = 90 b = 58.67 β = 90 c = 119.61 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.97840 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.91 41.881 100 0.092 0.101 0.04 0.999 2.2 11.2 16977
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 8.96 100 1.107 0.504 0.741 2.2 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1e9c 1.91 41.881 1.35 16913 798 99.96 0.221 0.2196 0.2269 0.2486 0.2519
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.893 f_angle_d 1.08 f_chiral_restr 0.072 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1506 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHENIX phasing