☰ Navigation Tabs
Crystal Structure of human thymidylate synthase bound to a peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YPV PDB ENTRY 1YPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 293 25% saturated Ammonium Sulfate, 20mM BME, 0.1M TRIS pH8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.9 57.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.109 α = 90 b = 96.109 β = 90 c = 82.24 γ = 120
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 2008-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.947 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.26 83.33 99.8 0.071 0.071 25.9 11 39745 1 2 45.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.38 100 0.303 0.303 6.7 11.2 5857
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1YPV 2.26 83.23 2 1 39745 37678 1990 99.72 0.2047 0.18939 0.18768 0.1831 0.22136 0.217 RANDOM 30.258
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 37.816 r_dihedral_angle_4_deg 17.694 r_dihedral_angle_3_deg 16.669 r_dihedral_angle_1_deg 6.821 r_scangle_it 3.74 r_scbond_it 2.315 r_mcangle_it 1.565 r_angle_refined_deg 1.496 r_mcbond_it 0.802 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.816 r_dihedral_angle_4_deg 17.694 r_dihedral_angle_3_deg 16.669 r_dihedral_angle_1_deg 6.821 r_scangle_it 3.74 r_scbond_it 2.315 r_mcangle_it 1.565 r_angle_refined_deg 1.496 r_mcbond_it 0.802 r_chiral_restr 0.11 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4339 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 20
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling