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Human Adenovirus type C5 knob protein with the KO1 mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Based on 1KNB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane, 20 % w/v PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.976 α = 90 b = 139.976 β = 90 c = 139.786 γ = 90
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 EIGER X 9M 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 2.6 57.2 100 0.389 0.403 0.106 0.988 6.1 14.5 82777
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 2.6 2.65 99.8 2.66 2.765 0.752 0.424 13.4
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 2.6 57.2 78394 4315 99.97 0.2163 0.21408 0.2177 0.25718 0.2605 RANDOM 44.834
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] -0.27 -0.27 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.714 r_dihedral_angle_3_deg 16.006 r_dihedral_angle_4_deg 14.618 r_dihedral_angle_1_deg 8.598 r_long_range_B_refined 6.737 r_long_range_B_other 6.718 r_mcangle_it 3.883 r_mcangle_other 3.882 r_scangle_other 3.523 r_scbond_it 2.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.714 r_dihedral_angle_3_deg 16.006 r_dihedral_angle_4_deg 14.618 r_dihedral_angle_1_deg 8.598 r_long_range_B_refined 6.737 r_long_range_B_other 6.718 r_mcangle_it 3.883 r_mcangle_other 3.882 r_scangle_other 3.523 r_scbond_it 2.366 r_scbond_other 2.366 r_mcbond_other 2.279 r_mcbond_it 2.278 r_angle_refined_deg 1.466 r_angle_other_deg 1.217 r_chiral_restr 0.066 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 8598 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing