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Marburg virus VP30 bound to nucleoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 20% isopropanol, 18% PEG 4000, 0.1M sodium citrate pH 5.6 using 0.2 uL 24.7 mg/mL protein mixed with 0.2 uL mother liquor
Crystal Properties Matthews coefficient Solvent content 3.79 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.143 α = 90 b = 106.143 β = 90 c = 375.573 γ = 120
Symmetry Space Group P 31 2 1
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 PILATUS3 S 6M 2016-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.750200 APS 23-ID-D
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 3.25 125.191 100 0.11 1 15.9 19.1 39861 126.6
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 3.25 3.38 100 2.96 0.61 1.1 19.5
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 5DVW 3.25 125.19 37850 1939 99.94 0.21401 0.21261 0.2056 0.24082 0.2348 RANDOM 143.111
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] 1.43 0.71 1.43 -4.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.808 r_scangle_other 18.965 r_dihedral_angle_3_deg 18.616 r_long_range_B_refined 17.554 r_long_range_B_other 17.554 r_scbond_it 15.223 r_scbond_other 15.221 r_mcangle_it 13.766 r_mcangle_other 13.765 r_mcbond_it 10.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 47.808 r_scangle_other 18.965 r_dihedral_angle_3_deg 18.616 r_long_range_B_refined 17.554 r_long_range_B_other 17.554 r_scbond_it 15.223 r_scbond_other 15.221 r_mcangle_it 13.766 r_mcangle_other 13.765 r_mcbond_it 10.208 r_mcbond_other 10.208 r_dihedral_angle_4_deg 8.149 r_dihedral_angle_1_deg 3.896 r_angle_other_deg 3.351 r_angle_refined_deg 1.142 r_chiral_restr 0.047 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 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 8624 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing