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Crystal Structure of Benzamide SNX-1321 bound to Hsp90
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D0B PDB ENTRY 3D0B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 6.5 277 Crystallized in 0.2M MgCl2, 0.1M Bis-Tris pH 6.5, and 20% PEG 3350 and were cryo-protected by adding 25% Ethylene Glycol to the mother liquor and passing the crystal through the solution immediately before flash freezing it in liquid nitrogen. The drops were setup by hand, adding 0.5ul protein to 0.5ul of reservoir in a sitting drop 192-well corning crystallization plate and incubated at 277K. , LIQUID DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.87 57.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.773 α = 90 b = 90.753 β = 90 c = 99.116 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113.5 CCD RIGAKU SATURN 92 2004-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 36.45 95 0.084 10.8 2.74 23062 21887 3 10.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 95 0.13 1.8 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3D0B 1.9 36.45 23062 21887 1175 95.56 0.19021 0.18784 0.192 0.23458 RANDOM 20.528
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] -0.24 0.7 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.964 r_dihedral_angle_4_deg 20.326 r_dihedral_angle_3_deg 12.74 r_dihedral_angle_1_deg 5.831 r_scangle_it 2.59 r_scbond_it 1.589 r_angle_refined_deg 1.302 r_mcangle_it 1.111 r_mcbond_it 0.671 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.964 r_dihedral_angle_4_deg 20.326 r_dihedral_angle_3_deg 12.74 r_dihedral_angle_1_deg 5.831 r_scangle_it 2.59 r_scbond_it 1.589 r_angle_refined_deg 1.302 r_mcangle_it 1.111 r_mcbond_it 0.671 r_nbtor_refined 0.301 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.125 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1644 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 35
Software Software Software Name Purpose CrystalClear data collection REFMAC refinement d*TREK data reduction d*TREK data scaling