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Adenovirus Serotype 26 (Ad26) in complex with sialic acid, pH4.0
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 4 291 0.1 M MIB [Malonic acid, Imidazole, Boric acid], 25 % w/v PEG 1500.
Crystal Properties Matthews coefficient Solvent content 2.19 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.731 α = 90 b = 85.731 β = 90 c = 85.731 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) 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 1.03 49.5 97.7 0.053 0.055 1 0.219 14.9 103975
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 1.03 1.06
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6FJN 1.03 49.5 96027 4907 97.65 0.13689 0.13632 0.14792 0.1418 RANDOM 17.636
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 36.535 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 7.441 r_rigid_bond_restr 7.239 r_long_range_B_refined 5.677 r_long_range_B_other 5.676 r_scangle_other 5.1 r_scbond_it 4.387 r_scbond_other 4.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.535 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 7.441 r_rigid_bond_restr 7.239 r_long_range_B_refined 5.677 r_long_range_B_other 5.676 r_scangle_other 5.1 r_scbond_it 4.387 r_scbond_other 4.385 r_mcangle_it 3.36 r_mcangle_other 3.359 r_mcbond_other 2.47 r_mcbond_it 2.469 r_angle_other_deg 2.396 r_angle_refined_deg 1.754 r_chiral_restr 0.108 r_bond_other_d 0.036 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.01 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 1504 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing