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Human Adenovirus type C5 knob protein with the KO1 mutation and A20 insertion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KNB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.2 M Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris propane, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.283 α = 90 b = 85.283 β = 90 c = 85.283 γ = 90
Symmetry Space Group P 21 3
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 2022-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
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 1.27 60.3 100 0.083 0.084 0.014 1 22.9 32.8 54652
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 1.27 1.29 99.2 2.24 2.386 0.789 0.353 0.4 8.6
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 (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 1.27 60.3 51794 2725 99.83 0.1573 0.15657 0.1645 0.17112 0.1801 RANDOM 17.784
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.003 r_dihedral_angle_3_deg 10.769 r_dihedral_angle_4_deg 7.805 r_dihedral_angle_1_deg 7.187 r_long_range_B_refined 4.34 r_long_range_B_other 3.95 r_scangle_other 1.875 r_angle_refined_deg 1.634 r_angle_other_deg 1.473 r_mcangle_it 1.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.003 r_dihedral_angle_3_deg 10.769 r_dihedral_angle_4_deg 7.805 r_dihedral_angle_1_deg 7.187 r_long_range_B_refined 4.34 r_long_range_B_other 3.95 r_scangle_other 1.875 r_angle_refined_deg 1.634 r_angle_other_deg 1.473 r_mcangle_it 1.416 r_mcangle_other 1.415 r_scbond_it 1.205 r_scbond_other 1.204 r_mcbond_it 0.855 r_mcbond_other 0.855 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 1360 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DIALS data scaling XDS data reduction PHASER phasing