☰ Navigation Tabs
E. coli DHFR product complex with (6S)-5,6,7,8-TETRAHYDROFOLATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 20 mg/ml protein working stock was prepared from 2:1 v/v mixing of 30mg/ml protein in 20mM Tris pH 8, 1mM DTT and 50mM HEPES pH 7.3, 100mM NaCl. Then the working protein stock at 20 mg/ml is mixed at 1:1 v/v ratio with reservoir solution of 0.1M MES pH 6.5, 30% PEG3350, 0.4M MgCl2
Crystal Properties Matthews coefficient Solvent content 1.84 33.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.861 α = 90 b = 51.529 β = 90 c = 77.841 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 100 CCD RAYONIX MX-225 Diamond(111) 2017-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 1.03 31.057 97.3 0.064 12.57 6.354 65916 10.76
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 1.03 1.09 84.2 1.019 1.01 3.06
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7DFR 1.03 31.06 1.34 65896 1995 97.3 0.186 0.186 0.1805 0.206 0.2037 16.39
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 f_dihedral_angle_d 13.331 f_angle_d 1.387 f_chiral_restr 0.074 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1297 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction