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Flavin-dependent thymidylate synthase in complex with FAD and deoxyuridine
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 8 293.15 40-50% PEG 200, 0-150 mM NaCl, 100 mM Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.03 39.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.19 α = 90 b = 116.113 β = 90 c = 141.891 γ = 90
Symmetry Space Group P 21 21 21
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 2013-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.93 89.86 98.1 0.094 22.8 7.6 67137
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 1.93 89.86 62459 3318 96.17 0.1723 0.17072 0.1795 0.2018 0.2069 RANDOM 39.126
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] 1.3 -1 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.945 r_dihedral_angle_4_deg 15.9 r_dihedral_angle_3_deg 13.656 r_long_range_B_refined 7.288 r_long_range_B_other 7.288 r_dihedral_angle_1_deg 5.832 r_scangle_other 5.626 r_mcangle_it 3.821 r_mcangle_other 3.821 r_scbond_it 3.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.945 r_dihedral_angle_4_deg 15.9 r_dihedral_angle_3_deg 13.656 r_long_range_B_refined 7.288 r_long_range_B_other 7.288 r_dihedral_angle_1_deg 5.832 r_scangle_other 5.626 r_mcangle_it 3.821 r_mcangle_other 3.821 r_scbond_it 3.487 r_scbond_other 3.487 r_mcbond_it 2.656 r_mcbond_other 2.655 r_angle_refined_deg 1.475 r_angle_other_deg 1.121 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 7142 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 367
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing