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Crystal Structure of the oligomerization domain of Vp35 from Ebola virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 296 50 mM HEPES-NaOH pH 7.5, 2.5 M Na-acetate
Crystal Properties Matthews coefficient Solvent content 2.94 58.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.782 α = 90 b = 98.907 β = 90 c = 185.069 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2016-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0080 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.1 49.45 99.9 0.107 0.112 0.031 0.999 16 13 69399 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 98.9 1.633 1.703 0.477 0.558 12.4
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 6GBP 2.1 30 65799 3501 99.78 0.2123 0.2107 0.2157 0.2424 0.2457 RANDOM 56.177
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] 1.79 -0.55 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.144 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_4_deg 14.119 r_dihedral_angle_1_deg 4.243 r_angle_refined_deg 1.077 r_angle_other_deg 0.737 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.144 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_4_deg 14.119 r_dihedral_angle_1_deg 4.243 r_angle_refined_deg 1.077 r_angle_other_deg 0.737 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6669 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction