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Ebola VP30 and its inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289.15 20% PEG3350 and 200 mM ammonium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.177 α = 72.88 b = 54.042 β = 85.961 c = 83.265 γ = 71.779
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 EIGER2 S 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) 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 2.29 79.55 95.2 0.099 0.546 2.4 1.7 31319
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 2.29 2.37 95.5 0.547
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.29 48.52 29773 1546 95.14 0.221 0.2184 0.2256 0.2638 0.272 RANDOM 45.408
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] -0.004 0.007 -0.005 0.014 -0.002 -0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.868 r_lrange_other 10.685 r_lrange_it 10.684 r_dihedral_angle_6_deg 9.794 r_scangle_it 8.982 r_scangle_other 8.981 r_scbond_it 5.984 r_scbond_other 5.982 r_mcangle_it 5.667 r_mcangle_other 5.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.868 r_lrange_other 10.685 r_lrange_it 10.684 r_dihedral_angle_6_deg 9.794 r_scangle_it 8.982 r_scangle_other 8.981 r_scbond_it 5.984 r_scbond_other 5.982 r_mcangle_it 5.667 r_mcangle_other 5.666 r_dihedral_angle_2_deg 5.076 r_dihedral_angle_1_deg 4.596 r_mcbond_it 4.083 r_mcbond_other 4.073 r_angle_refined_deg 0.62 r_angle_other_deg 0.247 r_nbd_refined 0.201 r_chiral_restr_other 0.191 r_symmetry_nbd_other 0.186 r_symmetry_nbd_refined 0.176 r_nbtor_refined 0.167 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.067 r_chiral_restr 0.033 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4040 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing