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Adenovirus species D serotype 49 Fiber-Knob KO1 mutant
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 8 291 Molecular Dimensions, PACT Pemier Screen, condition D05 (0.1 M MMT [Malic acid, MES, Tris], pH 8.0, 25 % w/v PEG 1500)
Crystal Properties Matthews coefficient Solvent content 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.17 α = 90 b = 55.99 β = 112.47 c = 116.03 γ = 90
Symmetry Space Group P 1 2 1
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 2017-02-27 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) 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 2.45 57.07 99.3 0.097 0.994 9.2 3.7 45958 59.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.51 99.3 1.274 0.491 1.2 3.7
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 2.45 57.06 43733 2225 98.98 0.19577 0.19258 0.1956 0.25845 0.2592 RANDOM 76.9
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] 5.35 2.21 -5.63 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.944 r_dihedral_angle_3_deg 20.985 r_dihedral_angle_4_deg 15.562 r_dihedral_angle_1_deg 9.189 r_long_range_B_refined 7.711 r_long_range_B_other 7.71 r_mcangle_it 4.101 r_mcangle_other 4.101 r_scangle_other 3.825 r_mcbond_it 2.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.944 r_dihedral_angle_3_deg 20.985 r_dihedral_angle_4_deg 15.562 r_dihedral_angle_1_deg 9.189 r_long_range_B_refined 7.711 r_long_range_B_other 7.71 r_mcangle_it 4.101 r_mcangle_other 4.101 r_scangle_other 3.825 r_mcbond_it 2.559 r_mcbond_other 2.559 r_scbond_it 2.425 r_scbond_other 2.391 r_angle_refined_deg 2.002 r_angle_other_deg 1.272 r_chiral_restr 0.088 r_bond_refined_d 0.012 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 9318 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data reduction Aimless data scaling PHASER phasing