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Crystal structure of the complex of T.spiralis thymidylate synthase with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate, crystallized in the presence of N(5,10)-methylenetetrahydrofolate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 277 0.1M NaF pH 7.1, 19% PEG 3350, 0.02% NaN3
Crystal Properties Matthews coefficient Solvent content 2.07 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.29 α = 72.47 b = 52.78 β = 68.03 c = 63.92 γ = 61.15
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 2015-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.179 28.092 97.41 0.034 0.04 1 16.43 3.61 172936
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 1.179 1.21 89
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 FREE R-VALUE 4g9u 1.179 28.092 1.97 172936 1816 97.41 0.1379 0.1377 0.1385 0.1511 0.1514 23.8067
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 16.262 f_angle_d 1.086 f_chiral_restr 0.08 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4676 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 125
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction PHASER phasing