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Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other sambucus nigra agglutinin II tetragonal crystal from
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 15.5
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 from 1.55 20 40471 40471 2131 96.65 0.11885 0.11885 0.11654 0.1313 0.1631 0.175 RANDOM 14.239
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.911 r_dihedral_angle_4_deg 20.243 r_dihedral_angle_3_deg 12.097 r_sphericity_free 10.639 r_scangle_it 7.401 r_dihedral_angle_1_deg 7.273 r_scbond_it 5.642 r_sphericity_bonded 4.773 r_mcangle_it 4.344 r_mcbond_it 3.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.911 r_dihedral_angle_4_deg 20.243 r_dihedral_angle_3_deg 12.097 r_sphericity_free 10.639 r_scangle_it 7.401 r_dihedral_angle_1_deg 7.273 r_scbond_it 5.642 r_sphericity_bonded 4.773 r_mcangle_it 4.344 r_mcbond_it 3.835 r_rigid_bond_restr 2.853 r_mcbond_other 2.539 r_angle_refined_deg 1.925 r_angle_other_deg 1.063 r_symmetry_vdw_other 0.316 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.225 r_nbd_other 0.216 r_symmetry_hbond_refined 0.189 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.118 r_nbtor_other 0.093 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 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 1980 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 181
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling REFMAC phasing