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Sambucus nigra agglutinin II (SNA-II), tetragonal crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure of SNA-II, hexagonal 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 ADSC QUANTUM 4 2002-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.937 ESRF ID14-1
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 1.35 64.55 99.6 0.075 0.075 14 4.6 66690 66690 16.2
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 1.35 1.39 99.7 0.395 0.395 2.3 3.3 4901
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 MOLECULAR REPLACEMENT THROUGHOUT Structure of SNA-II, hexagonal crystal form 1.35 19.94 63280 63280 3366 99.51 0.16227 0.16227 0.1603 0.1602 0.20049 0.1986 RANDOM 24.002
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 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.355 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 12.231 r_sphericity_free 10.775 r_sphericity_bonded 8.51 r_scangle_it 8.041 r_dihedral_angle_1_deg 7.268 r_scbond_it 6.29 r_mcangle_it 5.117 r_mcbond_it 4.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.355 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 12.231 r_sphericity_free 10.775 r_sphericity_bonded 8.51 r_scangle_it 8.041 r_dihedral_angle_1_deg 7.268 r_scbond_it 6.29 r_mcangle_it 5.117 r_mcbond_it 4.204 r_rigid_bond_restr 4.083 r_angle_refined_deg 1.887 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.203 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.143 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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 1979 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling MOLREP phasing