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Crystal structure of Trichinella spiralis thymidylate synthase complexed with dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Tris-HCl, PEG 4K, Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.695 α = 85.31 b = 65.914 β = 85.33 c = 96.511 γ = 67.12
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 RAYONIX MX-225 2011-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 20 98 0.128 6.1 5 89350
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 96.5 0.644 4.9 4418
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 4EZ8 1.9 19.96 84834 4466 97.3 0.1674 0.1646 0.173 0.2201 0.2246 RANDOM 31.805
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] -0.3 -0.07 -0.55 0.13 0.65 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.537 r_dihedral_angle_4_deg 20.773 r_dihedral_angle_3_deg 16.268 r_dihedral_angle_1_deg 6.745 r_mcangle_it 2.453 r_angle_refined_deg 1.815 r_mcbond_it 1.609 r_mcbond_other 1.607 r_angle_other_deg 0.891 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.537 r_dihedral_angle_4_deg 20.773 r_dihedral_angle_3_deg 16.268 r_dihedral_angle_1_deg 6.745 r_mcangle_it 2.453 r_angle_refined_deg 1.815 r_mcbond_it 1.609 r_mcbond_other 1.607 r_angle_other_deg 0.891 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9318 Nucleic Acid Atoms Solvent Atoms 862 Heterogen Atoms 136
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PHASER phasing