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Structure of the distal domain of mouse adenovirus 2 fibre bound to N-acetyl-glucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 1.125 M lithium sulphate, 0.075 M HEPES-NaOH, 25% (v/v) glycerol, 10 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.35 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.41 α = 90 b = 163.41 β = 90 c = 163.41 γ = 90
Symmetry Space Group I 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 CCD MARMOSAIC 225 mm CCD 2014-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
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 28.9 100 0.101 0.998 13.2 7.9 48930
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 2.05 100 0.404 0.714 4.8 7.8
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 5NBH 2 28 46439 2409 99.94 0.16736 0.16538 0.1731 0.20513 0.2059 RANDOM 28.478
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 36.306 r_dihedral_angle_4_deg 20.542 r_dihedral_angle_3_deg 13.141 r_dihedral_angle_1_deg 6.567 r_long_range_B_refined 5.796 r_long_range_B_other 5.663 r_scangle_other 3.375 r_mcangle_it 2.886 r_mcangle_other 2.886 r_scbond_it 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.306 r_dihedral_angle_4_deg 20.542 r_dihedral_angle_3_deg 13.141 r_dihedral_angle_1_deg 6.567 r_long_range_B_refined 5.796 r_long_range_B_other 5.663 r_scangle_other 3.375 r_mcangle_it 2.886 r_mcangle_other 2.886 r_scbond_it 2.1 r_scbond_other 2.1 r_mcbond_it 1.737 r_mcbond_other 1.737 r_angle_refined_deg 1.444 r_angle_other_deg 0.859 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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 4497 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling