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Adenovirus Serotype 26 (Ad26) in complex with sialic acid, pH8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 0.1 M MIB, 25 % w/v PEG 1500, pH8.0
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.92 α = 90 b = 85.92 β = 90 c = 85.92 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 2018-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.91587 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.19 42.96 100 0.085 0.088 20.7 21.4 67799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.22
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 6FJN 1.19 42.96 64286 3441 100 0.14322 0.14176 0.141 0.17201 0.1718 RANDOM 29.632
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 37.468 r_long_range_B_other 34.402 r_long_range_B_refined 34.099 r_mcbond_other 33.582 r_mcbond_it 33.555 r_mcangle_it 30.079 r_mcangle_other 30.066 r_dihedral_angle_4_deg 22.828 r_scangle_other 21.025 r_scbond_it 18.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.468 r_long_range_B_other 34.402 r_long_range_B_refined 34.099 r_mcbond_other 33.582 r_mcbond_it 33.555 r_mcangle_it 30.079 r_mcangle_other 30.066 r_dihedral_angle_4_deg 22.828 r_scangle_other 21.025 r_scbond_it 18.006 r_scbond_other 17.996 r_dihedral_angle_3_deg 15.507 r_rigid_bond_restr 9.244 r_dihedral_angle_1_deg 7.068 r_angle_other_deg 2.339 r_angle_refined_deg 1.661 r_chiral_restr 0.089 r_bond_other_d 0.035 r_gen_planes_other 0.012 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1469 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing