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E. Coli Thymidylate Synthase Y209M mutant complexed with 5-nitro-dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2.5 M AMMONIUM SULFATE, 20 MM
REMARK 280 KH2PO4, 4 MM DTT, 4 MM
5-NO2-dUMP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.22 61.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.02 α = 90 b = 133.02 β = 90 c = 133.02 γ = 90
Symmetry Space Group I 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 DIFFRACTOMETER ENRAF-NONIUS FAST 1997-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.5418
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 2.2 35 93 0.081 0.081 7.5 5.1 19978 18431
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.46 99
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 FOURIER SYNTHESIS THROUGHOUT 3TMS 2.2 26.09 17489 942 92.26 0.16758 0.1651 0.1685 0.21799 0.2172 RANDOM 30.051
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 36.111 r_dihedral_angle_4_deg 22.342 r_dihedral_angle_3_deg 17.347 r_dihedral_angle_1_deg 6.421 r_scangle_it 4.217 r_scbond_it 2.656 r_mcangle_it 1.711 r_angle_refined_deg 1.657 r_mcbond_it 0.973 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.111 r_dihedral_angle_4_deg 22.342 r_dihedral_angle_3_deg 17.347 r_dihedral_angle_1_deg 6.421 r_scangle_it 4.217 r_scbond_it 2.656 r_mcangle_it 1.711 r_angle_refined_deg 1.657 r_mcbond_it 0.973 r_nbtor_refined 0.309 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.163 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2149 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MADNESS data collection PROCOR data reduction PROCOR data scaling