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Adenovirus species 48, fiber knob protein
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 6.5 293 0.1 M Bis-Tris-propane, 20% PEG 3350, 0.2M NaNO3
Crystal Properties Matthews coefficient Solvent content 2.92 57.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.205 α = 90 b = 145.205 β = 90 c = 145.205 γ = 90
Symmetry Space Group P 43 3 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 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 2.91 83.82 100 0.125 0.127 1 22.2 41.2 12061 74.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.91 2.99 100 3.026 3.063 0.705 41.4
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 1KNB 2.91 83.83 11371 572 99.4 0.20525 0.20083 0.2069 0.29134 0.2955 RANDOM 84.911
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 36.855 r_dihedral_angle_3_deg 21.371 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_1_deg 10.243 r_long_range_B_other 9.681 r_long_range_B_refined 9.68 r_mcangle_it 5.925 r_mcangle_other 5.923 r_scangle_other 5.872 r_scbond_it 3.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.855 r_dihedral_angle_3_deg 21.371 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_1_deg 10.243 r_long_range_B_other 9.681 r_long_range_B_refined 9.68 r_mcangle_it 5.925 r_mcangle_other 5.923 r_scangle_other 5.872 r_scbond_it 3.947 r_mcbond_it 3.75 r_mcbond_other 3.749 r_scbond_other 3.705 r_angle_refined_deg 2.293 r_angle_other_deg 1.217 r_chiral_restr 0.138 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3076 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing