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Structure of Grp94 bound to methyl 2-[2-(2-benzylpyridin-3-yl)ethyl]-3-chloro-4,6-dihydroxybenzoate, a pan-Hsp90 inhibitor
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, HANGING DROP 7.8 289.2 1:1 30 mg/mL protein in 100 mM bicine, pH 7.8 against mother liquor (37% PEG400, 5% glycerol, 100 mM bicine, pH 7.8, 75 mM magnesium chloride). Crystals were harvested, and soaked for 48 hours in mother liquor containing 2.5 mM inhibitor. After soaking, glycerol was added to ~25% final concentration.
Crystal Properties Matthews coefficient Solvent content 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.431 α = 90 b = 84.717 β = 90 c = 95.759 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 197.5 CCD MARMOSAIC 225 mm CCD 2016-10-21 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 2.35 42.36 100 0.09377 24.75 14.3 22770
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 2.35 2.434 0.4773
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 2.35 42.359 1.36 22739 1997 99.75 0.2001 0.1966 0.1968 0.2367 0.2364
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 17.278 f_angle_d 0.8 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3441 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 218
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing