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Crystal structure of mouse thymidylate synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RTS PDB entry 1RTS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 278 Tris-HCl pH 8.5, PEG 4000, Li2SO4, VAPOR DIFFUSION, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.35 63.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.202 α = 90 b = 87.962 β = 97.43 c = 68.043 γ = 90
Symmetry Space Group C 1 2 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 MAR CCD 165 mm 2008-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.038 MAX II I911-2
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 1.94 20 98.9 0.053 15 3.6 69498
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 1.94 1.97 98.7 0.617 3.4 3476
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 PDB entry 1RTS 1.94 19.48 67377 1366 98.52 0.221 0.22 0.2211 0.266 0.2596 RANDOM 41.367
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.347 r_dihedral_angle_4_deg 19.156 r_dihedral_angle_3_deg 16.479 r_dihedral_angle_1_deg 6.825 r_scangle_it 5.241 r_scbond_it 3.498 r_mcangle_it 2.388 r_angle_refined_deg 1.953 r_mcbond_it 1.378 r_chiral_restr 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.347 r_dihedral_angle_4_deg 19.156 r_dihedral_angle_3_deg 16.479 r_dihedral_angle_1_deg 6.825 r_scangle_it 5.241 r_scbond_it 3.498 r_mcangle_it 2.388 r_angle_refined_deg 1.953 r_mcbond_it 1.378 r_chiral_restr 0.152 r_bond_refined_d 0.026 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4553 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOLREP phasing