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E. coli DHFR substrate complex with Dihydrofolate
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 Sitting drop of final volume of 0.8 uL was set up by 1:1 v/v mixing of 15 mg/mL E. coli DHFR working stock with reservoir solution containing 0.1M MES pH 6.5, 27.5% PEG 3350, 0.4M MgCl2. E. coli DHFR working stock was prepared from a 1:1 v/v mixture of 30 mg/ml protein in 20 mM Tris pH 8, 1mM DTT with 50 mM HEPES pH 7.3, 100 mM NaCl. Crystals harvested after 2 weeks growth and cryoprotected with mitegen LV oil before flash freezing in N2.
Crystal Properties Matthews coefficient Solvent content 1.78 31.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.698 α = 90 b = 51.525 β = 90 c = 77.421 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) 2017-11-30 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) Rrim I (All) CC (Half) 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 1.108 30.949 97.9 0.067 0.073 0.999 13.44 6.255 53265 11.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.108 1.18 87.3 0.861 1.051 0.571 1.16 2.804
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 1.108 30.949 1.34 53202 1993 97.82 0.1792 0.1786 0.1793 0.1961 0.1958 18.63
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 13.574 f_angle_d 1.334 f_chiral_restr 0.078 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1328 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 60
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction