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Crystal structure of thymidylate synthase from Elizabethkingia anophelis NUHP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IX6 PDB entry 3IX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 23.2 mg/mL ElanA.00249.a.B1.PW38270 against MORPHEUS F9 (plate id 292618f9): 10% w/v PEG20000, 20% v/v PEG550 MME, 100 mM bicine/Trizma base, pH 8.5, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetryl-D-glucosamine, cryoprotection: direct, puck id zfj8-8
Crystal Properties Matthews coefficient Solvent content 2.22 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.11 α = 90 b = 78.55 β = 90.49 c = 73.37 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2017-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.7 50 99.7 0.056 0.064 0.997 13.36 4.301 89735 -3 28.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 100 0.576 0.669 0.819 2.01 3.848
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 PDB entry 3IX6 1.7 50 1.35 89704 2208 99.73 0.1576 0.1571 0.1581 0.1758 0.1764 39.899
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 13.409 f_angle_d 0.857 f_chiral_restr 0.054 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5964 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Coot model building