3CA1

Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to galactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthersambucus nigra agglutinin II tetragonal crystal from

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
11.5534.7496.60.0520.05221.54.4426444264415.5
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)
11.551.64780.1350.1357.12.74945

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 from1.55204047140471213196.650.118850.118850.116540.1631RANDOM14.239
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]
0.030.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.911
r_dihedral_angle_4_deg20.243
r_dihedral_angle_3_deg12.097
r_sphericity_free10.639
r_scangle_it7.401
r_dihedral_angle_1_deg7.273
r_scbond_it5.642
r_sphericity_bonded4.773
r_mcangle_it4.344
r_mcbond_it3.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.911
r_dihedral_angle_4_deg20.243
r_dihedral_angle_3_deg12.097
r_sphericity_free10.639
r_scangle_it7.401
r_dihedral_angle_1_deg7.273
r_scbond_it5.642
r_sphericity_bonded4.773
r_mcangle_it4.344
r_mcbond_it3.835
r_rigid_bond_restr2.853
r_mcbond_other2.539
r_angle_refined_deg1.925
r_angle_other_deg1.063
r_symmetry_vdw_other0.316
r_symmetry_vdw_refined0.252
r_nbd_refined0.225
r_nbd_other0.216
r_symmetry_hbond_refined0.189
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.164
r_chiral_restr0.118
r_nbtor_other0.093
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1980
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms181

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing