☰ Navigation Tabs
Adenovirus Type 5 Fiber Knob protein at 1.49A resolution
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 293 DL-Malic acid, MES monohydrate, Tris, pH 7.0 (condition D4 of PACT premier suite from Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 3.3 62.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.16 α = 90 b = 102.44 β = 90 c = 77.01 γ = 90
Symmetry Space Group P 21 21 21
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 2018-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96859 Diamond I24
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 1.49 61.56 99.8 0.134 0.159 0.983 7.1 6.6 131951 18.3
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 1.49 1.53 99.9 1.838 2.183 0.565 6.3
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 1.49 61.56 125479 6388 99.8 0.21201 0.21091 0.2102 0.23305 0.2313 RANDOM 30.628
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] 2.18 -1.47 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.531 r_sphericity_free 39.16 r_rigid_bond_restr 17.29 r_sphericity_bonded 14.296 r_dihedral_angle_3_deg 13.886 r_dihedral_angle_4_deg 12.118 r_dihedral_angle_1_deg 7.51 r_long_range_B_refined 2.691 r_long_range_B_other 2.242 r_scangle_other 1.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.531 r_sphericity_free 39.16 r_rigid_bond_restr 17.29 r_sphericity_bonded 14.296 r_dihedral_angle_3_deg 13.886 r_dihedral_angle_4_deg 12.118 r_dihedral_angle_1_deg 7.51 r_long_range_B_refined 2.691 r_long_range_B_other 2.242 r_scangle_other 1.697 r_mcangle_it 1.56 r_mcangle_other 1.56 r_angle_refined_deg 1.534 r_scbond_it 1.484 r_scbond_other 1.484 r_mcbond_it 1.181 r_mcbond_other 1.18 r_angle_other_deg 0.929 r_chiral_restr 0.08 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4310 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing