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Crystal structure of Grp94 bound to isoform-selective inhibitor methyl 2-(2-(1-(4-bromobenzyl)-1H-imidazol-2-yl)ethyl)-3-chloro-4,6-dihydroxybenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289.15 Protein at 30 mg/mL in 0.1 M Tris pH 7.5 was mixed 1:1 with mother liquor comprised of 35% PEG400, 0.1 M Tris pH 7.5, and 80 mM MgCl2.
Crystals were harvested and soaked in mother liquor containing 20 mM inhibitor. A layer of glycerol was then added through which crystals were harvested and cryo-cooled in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.51 50.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.237 α = 90 b = 84.42 β = 90 c = 95.473 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 80 CCD MARMOSAIC 300 mm CCD 2014-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 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 2.707 47.74 97.71 0.121 22.11 14.6 217928
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 2GFD 2.707 47.736 1.35 14528 1453 97.4 0.2076 0.1992 0.2013 0.2855 0.2843
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 15.588 f_angle_d 1.272 f_chiral_restr 0.049 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3307 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing