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Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre complexed with lacto-N-neo-tetraose
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 PH 8.0, 27% (W/V) POLY -ETHYLENE GLYCOL 3350, 200 MM LITHIUM NITRATE 5 MM DITHIOTHREITOL, 5 MM LACTO-N-NEO-TETRAOSE
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.42 α = 90 b = 38.79 β = 102.2 c = 84.4 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 CCD MARRESEARCH TWO CYLINDRICAL VERTICAL FOCUSING PARABOLIC MIRRORS 2009-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.9 40 98.5 0.06 12.6 3.4 23751 23
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 1.9 2 91.7 0.3 3.2 2.7
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 1.9 40 22538 1213 98.32 0.1894 0.18759 0.1895 0.22296 0.2273 RANDOM 32.697
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] 0.77 -1.35 -0.27 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_4_deg 24.803 r_dihedral_angle_3_deg 13.406 r_dihedral_angle_1_deg 6.821 r_scangle_it 4.76 r_scbond_it 3.454 r_mcangle_it 3.106 r_mcbond_it 2.21 r_angle_refined_deg 1.369 r_angle_other_deg 0.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_4_deg 24.803 r_dihedral_angle_3_deg 13.406 r_dihedral_angle_1_deg 6.821 r_scangle_it 4.76 r_scbond_it 3.454 r_mcangle_it 3.106 r_mcbond_it 2.21 r_angle_refined_deg 1.369 r_angle_other_deg 0.829 r_mcbond_other 0.815 r_symmetry_vdw_refined 0.266 r_symmetry_vdw_other 0.223 r_nbd_refined 0.206 r_nbd_other 0.201 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.095 r_nbtor_other 0.086 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 2347 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing