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Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F5U PDB ENTRY 6F5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 Molecular Dimensions/Calibre Morpheus screen A11: 10% (w/V) PEG 4000, 20% (V/V) glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM bicine/Trizma base pH 8.5: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml: over night soak with 1mM compound ARN0075146 (BSI110990): tray 313149a11, cryo: direct: puck hdp6-5
Crystal Properties Matthews coefficient Solvent content 3.38 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.17 α = 90 b = 114.17 β = 90 c = 308.72 γ = 120
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-300 Beryllium Lenses 2019-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 50 99.9 0.054 22.26 6.824 32679 54.11
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 2.41 100 0.565 2.96 6.91
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB ENTRY 6F5U 2.35 41.63 1.35 32635 2032 99.8 0.179 0.177 0.177 0.205 0.2045 0 65.07
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 12.3 f_angle_d 0.736 f_chiral_restr 0.048 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2768 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 158
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing