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Human adenovirus type 24 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 5 291 0.1 M MMT Buffer, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.15 42.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.259 α = 90 b = 99.619 β = 100.26 c = 113.549 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2019-10-17 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) Rpim 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 2.9 55.96 100 0.15 0.175 0.089 0.973 4.4 3.8 25128
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 100 1.117 1.296 0.649 0.652 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.1 55.87 19502 1004 99.89 0.23903 0.234 0.2328 0.33672 0.3298 RANDOM 93.976
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] 2.54 0.46 0.9 -3.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.245 r_dihedral_angle_3_deg 22.964 r_dihedral_angle_4_deg 18.843 r_dihedral_angle_1_deg 12.095 r_long_range_B_refined 3.644 r_long_range_B_other 3.644 r_mcangle_it 2.192 r_mcangle_other 2.192 r_scangle_other 1.632 r_angle_refined_deg 1.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.245 r_dihedral_angle_3_deg 22.964 r_dihedral_angle_4_deg 18.843 r_dihedral_angle_1_deg 12.095 r_long_range_B_refined 3.644 r_long_range_B_other 3.644 r_mcangle_it 2.192 r_mcangle_other 2.192 r_scangle_other 1.632 r_angle_refined_deg 1.371 r_mcbond_it 1.272 r_mcbond_other 1.272 r_angle_other_deg 1.053 r_scbond_it 0.908 r_scbond_other 0.907 r_chiral_restr 0.05 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 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 8946 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing