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Crystal structure of the Mengla Virus VP30 C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 Citric acid, Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.85 56.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.886 α = 90 b = 73.886 β = 90 c = 53.405 γ = 120
Symmetry Space Group P 32 1 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 PIXEL DECTRIS PILATUS3 S 6M 2019-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 50 100 0.995 56.96 19.9 32952
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 1.4 1.42 0.965
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5T3W 1.4 30.401 32902 1676 99.921 0.177 0.1768 0.1769 0.1822 0.1823 23.21
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] 0.007 0.003 0.007 -0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.504 r_dihedral_angle_4_deg 18.026 r_dihedral_angle_3_deg 12.544 r_scangle_it 7.264 r_lrange_it 7.105 r_scbond_it 5.265 r_dihedral_angle_1_deg 5.214 r_mcangle_it 2.623 r_mcbond_it 2.152 r_angle_refined_deg 1.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.504 r_dihedral_angle_4_deg 18.026 r_dihedral_angle_3_deg 12.544 r_scangle_it 7.264 r_lrange_it 7.105 r_scbond_it 5.265 r_dihedral_angle_1_deg 5.214 r_mcangle_it 2.623 r_mcbond_it 2.152 r_angle_refined_deg 1.837 r_nbtor_refined 0.318 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.16 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 988 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing