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Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075164
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 5 287 Molecular Dimensions / Calibre Proplex screen e2: 100mM sodium citrate pH 5.0, 8% (w/V) PEG 8000: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml + 1mM compound AN75164/BSI110991: tray 313199e2, cryo: 20% EG + 5mM compound: puck puk2-8
Crystal Properties Matthews coefficient Solvent content 3.38 63.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.4 α = 90 b = 114.4 β = 90 c = 307.89 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 2021-02-08 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 2.75 50 99.9 0.06 18.6 5.511 20588 66.76
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 2.75 2.82 100 0.597 2.84 5.66
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 2.75 47.16 1.35 20572 2085 99.9 0.188 0.183 0.1818 0.225 0.2205 0 79.7
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 12.608 f_angle_d 0.667 f_chiral_restr 0.065 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2704 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 150
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing PHENIX model building Coot model building