3CA0

Sambucus nigra agglutinin II (SNA-II), hexagonal crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AAIchain B of ricin, PDN entry 2AAI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293PROTEIN 16 MG/ML, AMMONIUM SULFATE 2.0 M, SODIUM ACETATE 100 mM, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
6.5281.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.204α = 90
b = 120.204β = 90
c = 177.34γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.937ESRFID14-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.951.395.50.0830.08313.75573085730829.5
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)RedundancyNumber Unique Reflections (All)
11.92700.3240.3242.12.15977

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTchain B of ricin, PDN entry 2AAI1.95205229652296276299.030.172590.172590.171460.19412RANDOM41.658
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]
0.780.390.78-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.937
r_dihedral_angle_4_deg18.639
r_dihedral_angle_3_deg12.748
r_dihedral_angle_1_deg7.444
r_scangle_it4.648
r_scbond_it3.052
r_angle_refined_deg1.907
r_mcangle_it1.696
r_angle_other_deg1.369
r_mcbond_it1.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.937
r_dihedral_angle_4_deg18.639
r_dihedral_angle_3_deg12.748
r_dihedral_angle_1_deg7.444
r_scangle_it4.648
r_scbond_it3.052
r_angle_refined_deg1.907
r_mcangle_it1.696
r_angle_other_deg1.369
r_mcbond_it1.323
r_symmetry_vdw_other0.393
r_mcbond_other0.31
r_nbd_other0.216
r_nbd_refined0.205
r_symmetry_hbond_refined0.199
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.156
r_chiral_restr0.131
r_symmetry_vdw_refined0.127
r_nbtor_other0.113
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1980
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms209

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing