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Crystal structure of Ebola virus VP30 C-terminus/RBBP6 peptide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VAP PDB entry 5VAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 18% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.6 α = 90 b = 45.6 β = 90 c = 158.71 γ = 90
Symmetry Space Group P 43 21 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 CCD NOIR-1 2017-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00003 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 43.83 100 0.05 0.05 0.3 30.4 16.7 27964 26.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.3 0.02 0.02 0.3 0.7 10.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5VAP 1.5 43.83 26511 1317 99.82 0.19109 0.18913 0.1896 0.23021 0.231 RANDOM 32.79
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.867 r_dihedral_angle_4_deg 11.034 r_dihedral_angle_3_deg 10.907 r_long_range_B_refined 8.699 r_long_range_B_other 8.633 r_scangle_other 7.507 r_mcangle_other 5.196 r_mcangle_it 5.191 r_scbond_it 4.974 r_scbond_other 4.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.867 r_dihedral_angle_4_deg 11.034 r_dihedral_angle_3_deg 10.907 r_long_range_B_refined 8.699 r_long_range_B_other 8.633 r_scangle_other 7.507 r_mcangle_other 5.196 r_mcangle_it 5.191 r_scbond_it 4.974 r_scbond_other 4.971 r_dihedral_angle_1_deg 4.932 r_mcbond_it 3.551 r_mcbond_other 3.525 r_angle_other_deg 0.845 r_angle_refined_deg 0.659 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1105 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing