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Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075231
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 287 Optimization condition around ProPlex screen, condition E1: 100mM sodium acetate / hydrochloride pH 4.8, 7.49% (w/V) PEG 8000, 100mM magnesium chloride: EbzaA.19907.a.HE11.PD38458 at 14.4mg/ml + 1mM BSI111592 / ARN00075231: tray 322840 h3: cryo: 25% EG + 1mM compound: puck sni3-8
Crystal Properties Matthews coefficient Solvent content 3.36 63.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.94 α = 90 b = 113.94 β = 90 c = 308.49 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 2021-10-08 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) Rrim I (All) CC (Half) 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 2.25 50 99.1 0.05 0.056 0.999 17.81 4.94 36679 56.829
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.31 91.8 0.606 0.71 0.73 1.66 3.208
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 2.25 31.92 1.35 36663 2075 99.07 0.181 0.1796 0.18 0.2033 0.2041 0 67.34
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 15.5627 f_angle_d 0.9071 f_chiral_restr 0.0537 f_bond_d 0.0087 f_plane_restr 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2752 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 203
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing