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Sambucus nigra aggutinin II. tetragonal crystal form- complexed to fucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAMBUCUS NIGRA AGGLUTININ ii 6 TETRGONAL 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 34.68 98.8 0.044 0.044 32.4 5.7 43501 43501 15.4
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 92.9 0.095 0.095 11.5 3.2 5890
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 6 TETRGONAL CRYSTAL FORM 1.55 20 41276 41276 2186 98.76 0.12485 0.12485 0.12265 0.1235 0.16707 0.1634 RANDOM 12.673
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] -0.13 -0.13 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 19.88 r_dihedral_angle_3_deg 11.935 r_sphericity_free 11.584 r_dihedral_angle_1_deg 7.2 r_scangle_it 5.782 r_sphericity_bonded 4.584 r_scbond_it 4.286 r_mcangle_it 2.776 r_mcbond_it 2.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 19.88 r_dihedral_angle_3_deg 11.935 r_sphericity_free 11.584 r_dihedral_angle_1_deg 7.2 r_scangle_it 5.782 r_sphericity_bonded 4.584 r_scbond_it 4.286 r_mcangle_it 2.776 r_mcbond_it 2.261 r_rigid_bond_restr 2.124 r_angle_refined_deg 2.026 r_angle_other_deg 1.072 r_mcbond_other 0.845 r_symmetry_vdw_other 0.342 r_symmetry_vdw_refined 0.28 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.225 r_nbd_other 0.213 r_nbtor_refined 0.17 r_chiral_restr 0.16 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 1978 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling REFMAC phasing