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Structure of molecular chaperone Grp94 bound to selective inhibitor methyl 3-chloro-2-(2-{2-[(4-fluorophenyl)methyl]phenyl}ethyl)-4,6-dihydroxybenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GFD PDB entry 2GFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 289 30 mg/mL protein in 100 mM bicine, pH 7.8 mixed 1:1 with mother liquor (35-39% PEG400, 7.5-10% glycerol, 100 mM bicine, pH 7.8, 75 mM magnesium chloride, crystals harvested into mother liquor + 2 mM inhibitor, soaked for 4 days. Afterward, glycerol was added to 25% and crystals were harvested and immediately cryocooled with liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.599 α = 90 b = 96.897 β = 90 c = 42.953 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 197.5 CCD MARMOSAIC 225 mm CCD 2017-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00000 APS 22-BM
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 2.76 39.27 98 0.02231 19.3 2 7358
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 2.76 2.863 0.2064
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 FREE R-VALUE PDB entry 2GFD 2.764 39.268 1.34 7331 388 98.39 0.211 0.2075 0.2173 0.2793 0.2793
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 19.375 f_angle_d 1.097 f_chiral_restr 0.055 f_bond_d 0.009 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1692 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing