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Crystal structure of Sambucus nigra agglutinin II (SNA-II)-tetragonal crystal form- complexed to alpha1 methylgalactose
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 37.78 96.9 0.058 0.058 17.2 4.7 42458 42458 25.2
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 77.2 0.216 0.216 4.3 3.1 4882
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 40281 40281 2125 96.62 0.135 0.135 0.1328 0.1394 0.17977 0.1851 RANDOM 25.219
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] 0.1 0.1 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.218 r_dihedral_angle_4_deg 20.511 r_dihedral_angle_3_deg 11.952 r_sphericity_free 9.476 r_scangle_it 7.833 r_dihedral_angle_1_deg 6.998 r_sphericity_bonded 6.827 r_scbond_it 5.875 r_mcangle_it 5.225 r_mcbond_it 4.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.218 r_dihedral_angle_4_deg 20.511 r_dihedral_angle_3_deg 11.952 r_sphericity_free 9.476 r_scangle_it 7.833 r_dihedral_angle_1_deg 6.998 r_sphericity_bonded 6.827 r_scbond_it 5.875 r_mcangle_it 5.225 r_mcbond_it 4.336 r_rigid_bond_restr 3.498 r_angle_refined_deg 1.825 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.144 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1976 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling REFMAC phasing