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Structure of thymidylate synthase ThyX complexed to a new inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CFA PDB ENTRY 2CFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 10% PEG 5000 MME, 12% isopropanol, 12% DMSO, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.975 α = 111.65 b = 120.585 β = 91.13 c = 128.249 γ = 90.18
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 ADSC QUANTUM 315r 2009-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9791 SOLEIL PROXIMA 1
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 2.59 35 92.6 0.069 10.7 2.25 120946 111996 2 2 61.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.75 93.4 0.524 1.8 2.25
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2CFA 2.59 34.21 120946 111995 5633 0.2132 0.2132 0.2106 0.2224 0.2613 0.2743 RANDOM 53.73
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] -5.7276 0.516 1.5743 11.5469 3.2882 -5.8193
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.18 t_omega_torsion 2.65 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_improper_torsion t_chiral_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.18 t_omega_torsion 2.65 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_improper_torsion t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25151 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 1252
Software Software Software Name Purpose ADSC data collection MOLREP phasing BUSTER refinement XDS data reduction XSCALE data scaling