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Sambucus nigra agglutinin II, tetragonal crystal form- complexed to lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Sambucus nigra agglutinin, 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 34.79 96.7 0.041 0.041 23 4.6 43092 43092 15.3
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 1.63 78.7 0.142 0.142 7.6 2.8 5002
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, tetragonal crystal form 1.55 20 40807 40807 2155 97.02 0.13272 0.13272 0.13032 0.1322 0.17896 0.1809 RANDOM 17.392
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.202 r_dihedral_angle_4_deg 20.248 r_dihedral_angle_3_deg 11.841 r_sphericity_free 8.817 r_scangle_it 7.763 r_dihedral_angle_1_deg 7.171 r_sphericity_bonded 6.241 r_scbond_it 6.056 r_mcangle_it 4.763 r_mcbond_it 3.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.202 r_dihedral_angle_4_deg 20.248 r_dihedral_angle_3_deg 11.841 r_sphericity_free 8.817 r_scangle_it 7.763 r_dihedral_angle_1_deg 7.171 r_sphericity_bonded 6.241 r_scbond_it 6.056 r_mcangle_it 4.763 r_mcbond_it 3.935 r_rigid_bond_restr 3.848 r_angle_refined_deg 1.781 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 1982 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling REFMAC phasing