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Crystal structure of Ebola virus VP30 and its peptide NPL3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.15 M Cesium chloride, 15% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.83 56.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.7 α = 72.96 b = 53.726 β = 81.278 c = 82.876 γ = 63.799
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 EIGER X 9M 2023-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97915 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.04 46.61 98.1 0.978 3.3 1.8 44381
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.09 96.8 0.393
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.04 46.6 44369 2083 98.09 0.231 0.2296 0.2343 0.2573 0.2635 51.397
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] 0.022 -0.049 0.014 -0.009 0.012 -0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.778 r_lrange_other 11.153 r_lrange_it 11.14 r_scangle_it 8.574 r_scangle_other 8.572 r_dihedral_angle_6_deg 8.236 r_mcangle_it 5.767 r_mcangle_other 5.767 r_scbond_it 5.412 r_scbond_other 5.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.778 r_lrange_other 11.153 r_lrange_it 11.14 r_scangle_it 8.574 r_scangle_other 8.572 r_dihedral_angle_6_deg 8.236 r_mcangle_it 5.767 r_mcangle_other 5.767 r_scbond_it 5.412 r_scbond_other 5.412 r_dihedral_angle_1_deg 4.226 r_mcbond_it 4.133 r_mcbond_other 4.13 r_dihedral_angle_2_deg 1.665 r_angle_refined_deg 0.716 r_angle_other_deg 0.285 r_nbd_refined 0.2 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.163 r_nbd_other 0.14 r_symmetry_nbd_refined 0.136 r_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.067 r_symmetry_xyhbond_nbd_refined 0.051 r_chiral_restr_other 0.046 r_chiral_restr 0.041 r_symmetry_xyhbond_nbd_other 0.034 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4217 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing