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E. COLI THYMIDYLATE SYNTHASE IN SYMMETRIC COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KCE ONE MONOMER OF PDB ENTRY 1KCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.82 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.96 α = 90 b = 71.96 β = 90 c = 115.1 γ = 120
Symmetry Space Group P 31 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 287 IMAGE PLATE RIGAKU RAXIS IIC COLLIMATOR 1995-11-29 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 1.9 50 77.4 0.097 0.097 14.2 3.1 37807 1 8.1
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 1.9 1.98 45 0.275 0.321 3.1 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT ONE MONOMER OF PDB ENTRY 1KCE 1.9 7 2 20071 1995 73.9 0.18 0.18 0.23 RANDOM 20.9
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 x_dihedral_angle_d 24.5 x_scangle_it 4.91 x_mcangle_it 3.44 x_scbond_it 3.37 x_mcbond_it 2.51 x_angle_deg 1.5 x_improper_angle_d 1.18 x_bond_d 0.007 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.5 x_scangle_it 4.91 x_mcangle_it 3.44 x_scbond_it 3.37 x_mcbond_it 2.51 x_angle_deg 1.5 x_improper_angle_d 1.18 x_bond_d 0.007 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2153 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 55
Software Software Software Name Purpose AMoRE phasing X-PLOR refinement DENZO data reduction SCALEPACK data scaling