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Structure of human adenovirus serotype 37 fibre head in complex with a sialic acid derivative, O-Methyl 5-N-propaonyl-3,5-dideoxy-D- glycero-a-D-galacto-2-nonulopyranosylonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UXA PDB ENTRY 1UXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 25-27 % POLYETHYLENE GLYCOL 8000, 50 MM ZINC ACETATE, AND 100 MM HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.43 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.27 α = 90 b = 69.99 β = 94.42 c = 75 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 CCD ADSC CCD 2008-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 30 99.8 0.04 18.4 3.74 58545
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.8 0.47 2.88 3.73
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 PDB ENTRY 1UXA 1.8 30 55584 2953 99.8 0.185 0.183 0.1861 0.226 0.2284 RANDOM 19.36
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] 0.64 0.58 0.64 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.63 r_dihedral_angle_3_deg 12.066 r_dihedral_angle_4_deg 9.781 r_dihedral_angle_1_deg 6.533 r_scangle_it 1.922 r_scbond_it 1.337 r_angle_refined_deg 1.225 r_mcangle_it 1.094 r_angle_other_deg 0.864 r_mcbond_it 0.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.63 r_dihedral_angle_3_deg 12.066 r_dihedral_angle_4_deg 9.781 r_dihedral_angle_1_deg 6.533 r_scangle_it 1.922 r_scbond_it 1.337 r_angle_refined_deg 1.225 r_mcangle_it 1.094 r_angle_other_deg 0.864 r_mcbond_it 0.655 r_symmetry_vdw_refined 0.237 r_nbd_other 0.184 r_nbtor_refined 0.172 r_nbd_refined 0.171 r_metal_ion_refined 0.161 r_xyhbond_nbd_refined 0.135 r_symmetry_vdw_other 0.135 r_mcbond_other 0.129 r_symmetry_hbond_refined 0.125 r_nbtor_other 0.082 r_chiral_restr 0.074 r_symmetry_metal_ion_refined 0.023 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4361 Nucleic Acid Atoms Solvent Atoms 715 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing