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Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre complexed with lactose
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, 1 MM EDTA, 28% (W/V) POLY-ETHYLENE GLYCOL 3350, 100 MM SODIUM NITRATE, 5 MM DITHIOTHREITOL, 70 MM LACTOSE
Crystal Properties Matthews coefficient Solvent content 2.05 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.62 α = 90 b = 38.78 β = 93.53 c = 70.19 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 2 40 99.6 0.07 10.4 3.5 21094 23.4
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 2.11 99.3 0.32 3.3 3.5
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 40 20006 1087 99.66 0.18498 0.18252 0.1896 0.22752 0.2311 RANDOM 26.951
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] 1.8 -2.32 -1.41 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.013 r_dihedral_angle_4_deg 19.684 r_dihedral_angle_3_deg 13.149 r_dihedral_angle_1_deg 6.956 r_scangle_it 4.356 r_scbond_it 3.265 r_mcangle_it 2.95 r_mcbond_it 2.072 r_angle_refined_deg 1.309 r_angle_other_deg 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.013 r_dihedral_angle_4_deg 19.684 r_dihedral_angle_3_deg 13.149 r_dihedral_angle_1_deg 6.956 r_scangle_it 4.356 r_scbond_it 3.265 r_mcangle_it 2.95 r_mcbond_it 2.072 r_angle_refined_deg 1.309 r_angle_other_deg 0.79 r_mcbond_other 0.741 r_symmetry_vdw_refined 0.26 r_symmetry_vdw_other 0.218 r_nbd_refined 0.2 r_nbd_other 0.196 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.085 r_nbtor_other 0.084 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 184 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing