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Ebola virus VP40 octameric ring generated by a DNA 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 6.6 293 1 uL 3.5 mg/mL protein, 1 uL 75 mM sodium citrate tribasic pH 6.6, 150 mM ammonium acetate
Crystal Properties Matthews coefficient Solvent content 1.28 4.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.438 α = 90 b = 80.438 β = 90 c = 47.281 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 100.5 PIXEL DECTRIS PILATUS 6M 2019-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 1.78 40.76 99.9 0.098 0.998 15.5 12.3 15385 27.05
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 1.78 1.82 98.8 1.411 0.874 2.4 11.8
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 1.78 40.76 1.35 15377 757 99.84 0.1827 0.1819 0.1847 0.1981 0.1999 33.5
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 12.9439 f_angle_d 0.9286 f_chiral_restr 0.0572 f_bond_d 0.0071 f_plane_restr 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 942 Nucleic Acid Atoms 62 Solvent Atoms 86 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building