3CA5

Crystal structure of Sambucus nigra agglutinin II (SNA-II)-tetragonal crystal form- complexed to alpha1 methylgalactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSambucus nigra agglutinin II - tetragonal crystal form

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
2.6753.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.124α = 90
b = 126.124β = 90
c = 76.039γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2003-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9795ESRFBM30A

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
11.5537.7896.90.0580.05817.24.7424584245825.2
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)RedundancyNumber Unique Reflections (All)
11.551.6477.20.2160.2164.33.14882

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTSambucus nigra agglutinin II - tetragonal crystal form1.55204028140281212596.620.1350.1350.13280.17977RANDOM25.219
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]
0.10.1-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.218
r_dihedral_angle_4_deg20.511
r_dihedral_angle_3_deg11.952
r_sphericity_free9.476
r_scangle_it7.833
r_dihedral_angle_1_deg6.998
r_sphericity_bonded6.827
r_scbond_it5.875
r_mcangle_it5.225
r_mcbond_it4.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.218
r_dihedral_angle_4_deg20.511
r_dihedral_angle_3_deg11.952
r_sphericity_free9.476
r_scangle_it7.833
r_dihedral_angle_1_deg6.998
r_sphericity_bonded6.827
r_scbond_it5.875
r_mcangle_it5.225
r_mcbond_it4.336
r_rigid_bond_restr3.498
r_angle_refined_deg1.825
r_nbtor_refined0.313
r_symmetry_hbond_refined0.237
r_nbd_refined0.216
r_symmetry_vdw_refined0.2
r_xyhbond_nbd_refined0.185
r_chiral_restr0.144
r_bond_refined_d0.021
r_gen_planes_refined0.01
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 AtomsNumber
Protein Atoms1976
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms173

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing