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Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre complexed with tri(N-acetyl-lactosamine)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WSU PDB ENTRY 2WSU, CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 10 MM TRIS-HCL, 1 MM EDTA, 28% (W/V) POLY-ETHYLENE GLYCOL 3350, 300 MM LITHIUM NITRATE, 5 MM DITHIOTHREITOL, 5 MM TRI(N-ACETYL-LACTOSAMINE), PH 8.0
Crystal Properties Matthews coefficient Solvent content 1.9 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.13 α = 90 b = 38.26 β = 92.12 c = 86.52 γ = 90
Symmetry Space Group C 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 IMAGE PLATE MAR555 FLAT PANEL BENT, VERTICALLY FOCUSSING MIRROR 2009-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.5 40 99.9 0.1 8.8 3.6 20441 2 44.8
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 2.5 2.64 99.8 0.43 3.1 3.6
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 2WSU, CHAIN A 2.5 35 19313 1123 100 0.20365 0.19989 0.1982 0.2679 0.2636 THIN SHELLS 26.572
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] -1.01 -0.34 -2.17 3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_3_deg 13.329 r_dihedral_angle_1_deg 6.902 r_scangle_it 4.226 r_mcangle_it 2.95 r_scbond_it 2.906 r_mcbond_it 1.875 r_angle_refined_deg 1.274 r_angle_other_deg 0.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_3_deg 13.329 r_dihedral_angle_1_deg 6.902 r_scangle_it 4.226 r_mcangle_it 2.95 r_scbond_it 2.906 r_mcbond_it 1.875 r_angle_refined_deg 1.274 r_angle_other_deg 0.783 r_mcbond_other 0.508 r_symmetry_vdw_other 0.206 r_nbd_other 0.185 r_nbd_refined 0.181 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.167 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.148 r_nbtor_other 0.081 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 4708 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing