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Structure of the VP40 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Magnesium chloride hexahydrate 0.1M Tris
pH8.5, 25% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.031 α = 90 b = 90.812 β = 97.816 c = 49.22 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2021-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.35 48.76 99.1 0.076 10.9 4.1 11721
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 0.616
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 2.35 45.447 11720 566 98.911 0.176 0.1739 0.1803 0.2229 0.2306 43.518
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] 0.669 -1.574 -2.31 1.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.025 r_dihedral_angle_3_deg 11.203 r_lrange_it 7.611 r_lrange_other 7.6 r_dihedral_angle_1_deg 7.35 r_dihedral_angle_2_deg 6.608 r_scangle_it 4.994 r_scangle_other 4.992 r_mcangle_it 4.401 r_mcangle_other 4.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.025 r_dihedral_angle_3_deg 11.203 r_lrange_it 7.611 r_lrange_other 7.6 r_dihedral_angle_1_deg 7.35 r_dihedral_angle_2_deg 6.608 r_scangle_it 4.994 r_scangle_other 4.992 r_mcangle_it 4.401 r_mcangle_other 4.401 r_scbond_it 2.993 r_scbond_other 2.992 r_mcbond_it 2.742 r_mcbond_other 2.737 r_angle_refined_deg 1.215 r_angle_other_deg 0.393 r_symmetry_xyhbond_nbd_refined 0.227 r_nbd_refined 0.196 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.167 r_symmetry_nbd_refined 0.157 r_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.082 r_nbd_other 0.078 r_chiral_restr 0.054 r_bond_refined_d 0.004 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 1884 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing