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Ebola virus VP40 octameric ring generated by an RNA oligonucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LDM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 293 1 uL 3.5 mg/mL protein, 1 uL 75 mM sodium citrate tribasic pH 8.4, 150 mM ammonium acetate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.626 α = 90 b = 80.626 β = 90 c = 47.083 γ = 90
Symmetry Space Group P 4 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 100 PIXEL DECTRIS PILATUS3 S 6M 2019-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.38 80.63 95.7 0.059 0.999 27.8 24.8 30977 18.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.41 100 1.519 0.853 2.4 25.7
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 4LDM 1.38 23.54 1.34 30944 1555 95.62 0.181 0.1802 0.1841 0.197 0.1998 27.21
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 8.8708 f_angle_d 0.7841 f_chiral_restr 0.0716 f_plane_restr 0.0058 f_bond_d 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 950 Nucleic Acid Atoms 65 Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building