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Flavin-dependent thymidylate synthase in complex with FAD and 2'-deoxyuridine-5'-monosulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.6 293.15 7% PEG 4K, 100 mM NaCl, 100 mM Na/K phosphate, pH 6.6
Crystal Properties Matthews coefficient Solvent content 3.28 62.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.679 α = 90 b = 109.679 β = 90 c = 119.864 γ = 90
Symmetry Space Group I 41 2 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 CCD MARMOSAIC 300 mm CCD 2013-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03320 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 80.92 99.7 20.4 14.6 27043
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 4GT9 1.95 80.92 25671 1270 99.99 0.16341 0.16204 0.173 0.19148 0.2013 RANDOM 32.196
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] -0.99 -0.99 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.313 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 13.055 r_dihedral_angle_1_deg 6.017 r_long_range_B_refined 5.041 r_long_range_B_other 4.986 r_scangle_other 2.844 r_scbond_it 1.747 r_mcangle_it 1.742 r_mcangle_other 1.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.313 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 13.055 r_dihedral_angle_1_deg 6.017 r_long_range_B_refined 5.041 r_long_range_B_other 4.986 r_scangle_other 2.844 r_scbond_it 1.747 r_mcangle_it 1.742 r_mcangle_other 1.741 r_scbond_other 1.734 r_angle_refined_deg 1.342 r_mcbond_it 1.12 r_mcbond_other 1.12 r_angle_other_deg 0.786 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1801 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing