☰ Navigation Tabs
Sambucus nigra agglutinin II (SNA-II), hexagonal crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AAI chain B of ricin, PDN entry 2AAI
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 6.52 81.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.204 α = 90 b = 120.204 β = 90 c = 177.34 γ = 120
Symmetry Space Group P 64 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 1.9 51.3 95.5 0.083 0.083 13.7 5 57308 57308 29.5
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 1.9 2 70 0.324 0.324 2.1 2.1 5977
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 chain B of ricin, PDN entry 2AAI 1.95 20 52296 52296 2762 99.03 0.17259 0.17259 0.17146 0.181 0.19412 0.2014 RANDOM 41.658
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] 0.78 0.39 0.78 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.937 r_dihedral_angle_4_deg 18.639 r_dihedral_angle_3_deg 12.748 r_dihedral_angle_1_deg 7.444 r_scangle_it 4.648 r_scbond_it 3.052 r_angle_refined_deg 1.907 r_mcangle_it 1.696 r_angle_other_deg 1.369 r_mcbond_it 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.937 r_dihedral_angle_4_deg 18.639 r_dihedral_angle_3_deg 12.748 r_dihedral_angle_1_deg 7.444 r_scangle_it 4.648 r_scbond_it 3.052 r_angle_refined_deg 1.907 r_mcangle_it 1.696 r_angle_other_deg 1.369 r_mcbond_it 1.323 r_symmetry_vdw_other 0.393 r_mcbond_other 0.31 r_nbd_other 0.216 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.199 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.131 r_symmetry_vdw_refined 0.127 r_nbtor_other 0.113 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1980 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling MOLREP phasing