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Flavin-dependent thymidylate synthase R174A variant in complex with FAD and dUMP
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 2.01 38.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.06 α = 90 b = 115.86 β = 90 c = 141.1 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 2013-08-14 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) 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 2 89.54 90.7 8.7 6 54863
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 2 89.54 52046 2753 90.21 0.1845 0.18277 0.1911 0.21742 0.2219 RANDOM 34.545
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] -0.78 1.9 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.458 r_dihedral_angle_4_deg 19.737 r_dihedral_angle_3_deg 14.523 r_dihedral_angle_1_deg 5.932 r_long_range_B_refined 5.812 r_long_range_B_other 5.777 r_scangle_other 4.299 r_mcangle_it 2.841 r_mcangle_other 2.841 r_scbond_it 2.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.458 r_dihedral_angle_4_deg 19.737 r_dihedral_angle_3_deg 14.523 r_dihedral_angle_1_deg 5.932 r_long_range_B_refined 5.812 r_long_range_B_other 5.777 r_scangle_other 4.299 r_mcangle_it 2.841 r_mcangle_other 2.841 r_scbond_it 2.706 r_scbond_other 2.706 r_mcbond_it 1.955 r_mcbond_other 1.955 r_angle_refined_deg 1.489 r_angle_other_deg 1.198 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 7168 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 292
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing