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Crystal structure of Ebola Zaire envelope glycoprotein GP in complex with compound ARN75092
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 Proplex E2: 8% PEG8000, 0.1 M citrate, pH 5.0, 6.9 mg/mL EbzaA.19907.a.HE11.PD38351, plate: 12752-well E2 drop 2, Puck: PSL-1001, cryoprotectant: 16% PEG8000, 20% glycerol, 0.08 M citrate, pH 5.0, originally obtained from the complex with ARN75231, crystals were soaked in 5 mM ARN75092, 16% PEG8000, 0.1 M citrate, pH 5.0 for 24 hours before freezing
Crystal Properties Matthews coefficient Solvent content 3.68 66.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.199 α = 90 b = 113.199 β = 90 c = 306.021 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 291 PIXEL DECTRIS EIGER2 XE 9M 2022-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97949 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.6 93.36 100 0.101 0.103 0.022 0.999 22.2 21.3 23674
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 100 1.406 1.44 0.312 0.928 21.2
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 PDB entry 6NAE 2.6 51 1.34 23620 1113 99.78 0.2181 0.2176 0.2212 0.2282 0.2285
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 15.321 f_angle_d 0.581 f_chiral_restr 0.048 f_plane_restr 0.007 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2710 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 151
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing