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Crystal structure of Sambucus Nigra Agglutinin II (SNA-II)-tetragonal crystal form- complexed to N-Acetylgalactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Sambucus nigra agglutinin II, tetragonal crystal form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 PROTEIN 16 MG/ML, AMMONIUM SULFATE 2.0 M, SODIUM ACETATE 100 mM, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.124 α = 90 b = 126.124 β = 90 c = 76.039 γ = 90
Symmetry Space Group I 41 2 2
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 MAR CCD 165 mm 2003-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9795 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.55 34.74 96.6 0.052 0.052 21.5 4.4 42644 42644 14.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.64 78 0.135 0.135 7.1 2.7 4945
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT Sambucus nigra agglutinin II, tetragonal crystal form 1.55 20 40982 40982 2179 97.71 0.12451 0.12451 0.12197 0.1247 0.1731 0.1748 RANDOM 14.324
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.622 r_dihedral_angle_4_deg 22.391 r_dihedral_angle_3_deg 11.69 r_sphericity_free 10.733 r_scangle_it 7.689 r_dihedral_angle_1_deg 7.236 r_scbond_it 5.87 r_sphericity_bonded 5.037 r_mcangle_it 4.587 r_mcbond_it 4.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.622 r_dihedral_angle_4_deg 22.391 r_dihedral_angle_3_deg 11.69 r_sphericity_free 10.733 r_scangle_it 7.689 r_dihedral_angle_1_deg 7.236 r_scbond_it 5.87 r_sphericity_bonded 5.037 r_mcangle_it 4.587 r_mcbond_it 4.005 r_rigid_bond_restr 2.962 r_mcbond_other 2.672 r_angle_refined_deg 1.857 r_angle_other_deg 1.059 r_symmetry_vdw_other 0.295 r_nbd_refined 0.227 r_nbd_other 0.221 r_symmetry_vdw_refined 0.215 r_symmetry_hbond_refined 0.192 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.127 r_nbtor_other 0.11 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1984 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 217
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling REFMAC phasing