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Mouse thymidylate synthase in ternary complex with FdUMP and methylenetetrahydrofolate.
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 280 MES, PEG 8K, MgAcetate
Crystal Properties Matthews coefficient Solvent content 2.14 42.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.224 α = 90 b = 83.302 β = 105.43 c = 68.85 γ = 90
Symmetry Space Group P 1 21 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 AGILENT ATLAS CCD 2013-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.5406
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 1.55 26.14 99.97 0.068 14 5.9 85416
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 1.55 1.63 100 0.517 2.4 4
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 4EZ8 1.55 26.14 81162 4277 99.97 0.11972 0.11726 0.16614 0.1687 RANDOM 17.752
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] -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.039 r_sphericity_free 27.562 r_dihedral_angle_4_deg 18.898 r_dihedral_angle_3_deg 12.359 r_sphericity_bonded 9.844 r_dihedral_angle_1_deg 6.077 r_long_range_B_refined 3.885 r_long_range_B_other 3.222 r_scangle_other 2.883 r_scbond_it 2.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.039 r_sphericity_free 27.562 r_dihedral_angle_4_deg 18.898 r_dihedral_angle_3_deg 12.359 r_sphericity_bonded 9.844 r_dihedral_angle_1_deg 6.077 r_long_range_B_refined 3.885 r_long_range_B_other 3.222 r_scangle_other 2.883 r_scbond_it 2.459 r_scbond_other 2.458 r_mcangle_it 1.914 r_mcangle_other 1.914 r_rigid_bond_restr 1.841 r_mcbond_other 1.493 r_mcbond_it 1.492 r_angle_refined_deg 1.415 r_angle_other_deg 0.775 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4638 Nucleic Acid Atoms Solvent Atoms 661 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling CrysalisPro phasing