3CA4

Sambucus nigra agglutinin II, tetragonal crystal form- complexed to lactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSambucus nigra agglutinin, 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
11.5534.7996.70.0410.041234.6430924309215.3
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)
11.551.6378.70.1420.1427.62.85002

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, tetragonal crystal form1.55204080740807215597.020.132720.132720.130320.17896RANDOM17.392
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.202
r_dihedral_angle_4_deg20.248
r_dihedral_angle_3_deg11.841
r_sphericity_free8.817
r_scangle_it7.763
r_dihedral_angle_1_deg7.171
r_sphericity_bonded6.241
r_scbond_it6.056
r_mcangle_it4.763
r_mcbond_it3.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.202
r_dihedral_angle_4_deg20.248
r_dihedral_angle_3_deg11.841
r_sphericity_free8.817
r_scangle_it7.763
r_dihedral_angle_1_deg7.171
r_sphericity_bonded6.241
r_scbond_it6.056
r_mcangle_it4.763
r_mcbond_it3.935
r_rigid_bond_restr3.848
r_angle_refined_deg1.781
r_nbtor_refined0.32
r_symmetry_vdw_refined0.251
r_nbd_refined0.213
r_symmetry_hbond_refined0.207
r_xyhbond_nbd_refined0.155
r_chiral_restr0.126
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms1982
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms196

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing