☰ Navigation Tabs
Crystal structure of thymidylate synthase from Corynebacterium glutamicum in complex with dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2M magnesium chloride, 0.1M Tris-HCl, 21% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.042 α = 90 b = 87.815 β = 90 c = 165.747 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 2.75 30 99.9 0.115 8 27894
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 2.75 2.85 100 0.446 5.08 8.1 2911
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 4H0R 2.75 30 27894 1516 99.5 0.18934 0.18653 0.1882 0.24112 0.1869 RANDOM 31.959
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] -0.98 0.64 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.777 r_dihedral_angle_4_deg 23.576 r_dihedral_angle_3_deg 21.363 r_dihedral_angle_1_deg 8.228 r_scangle_it 3.417 r_scbond_it 2.067 r_mcangle_it 1.452 r_angle_refined_deg 1.344 r_mcbond_it 0.753 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.777 r_dihedral_angle_4_deg 23.576 r_dihedral_angle_3_deg 21.363 r_dihedral_angle_1_deg 8.228 r_scangle_it 3.417 r_scbond_it 2.067 r_mcangle_it 1.452 r_angle_refined_deg 1.344 r_mcbond_it 0.753 r_chiral_restr 0.103 r_bond_refined_d 0.017 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8264 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 80
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling