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Crystal structure of 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, SITTING DROP 293 0.2M Ammonium Sulfate , 0.1M Sodium, Acetate pH4.6, 25% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.87 57.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.062 α = 90 b = 73.062 β = 90 c = 53.459 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 6M 2019-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
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 1.34 40.87 99.9 0.06541 0.07254 0.03027 0.993 16.27 5.4 36367
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 1.344 1.392 0.4376 0.4909 0.2158 0.852 2.82
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 5T3W 1.34 40.87 34575 1792 99.88 0.12848 0.12705 0.1267 0.15496 0.1543 RANDOM 23.282
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] -0.5 -0.25 -0.5 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.228 r_dihedral_angle_4_deg 13.829 r_dihedral_angle_3_deg 10.737 r_scbond_it 9.982 r_scbond_other 9.927 r_scangle_other 9.181 r_rigid_bond_restr 6.14 r_long_range_B_refined 5.003 r_dihedral_angle_1_deg 4.765 r_long_range_B_other 4.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.228 r_dihedral_angle_4_deg 13.829 r_dihedral_angle_3_deg 10.737 r_scbond_it 9.982 r_scbond_other 9.927 r_scangle_other 9.181 r_rigid_bond_restr 6.14 r_long_range_B_refined 5.003 r_dihedral_angle_1_deg 4.765 r_long_range_B_other 4.532 r_mcangle_other 2.488 r_mcangle_it 2.472 r_mcbond_it 2.246 r_mcbond_other 1.994 r_angle_refined_deg 1.325 r_angle_other_deg 1.288 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1008 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing