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
11.5534.7496.60.0520.05221.54.4426444264414.2
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)
11.551.64780.1350.1357.12.74945

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 form1.55204098240982217997.710.124510.124510.121970.1731RANDOM14.324
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.622
r_dihedral_angle_4_deg22.391
r_dihedral_angle_3_deg11.69
r_sphericity_free10.733
r_scangle_it7.689
r_dihedral_angle_1_deg7.236
r_scbond_it5.87
r_sphericity_bonded5.037
r_mcangle_it4.587
r_mcbond_it4.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.622
r_dihedral_angle_4_deg22.391
r_dihedral_angle_3_deg11.69
r_sphericity_free10.733
r_scangle_it7.689
r_dihedral_angle_1_deg7.236
r_scbond_it5.87
r_sphericity_bonded5.037
r_mcangle_it4.587
r_mcbond_it4.005
r_rigid_bond_restr2.962
r_mcbond_other2.672
r_angle_refined_deg1.857
r_angle_other_deg1.059
r_symmetry_vdw_other0.295
r_nbd_refined0.227
r_nbd_other0.221
r_symmetry_vdw_refined0.215
r_symmetry_hbond_refined0.192
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.15
r_chiral_restr0.127
r_nbtor_other0.11
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1984
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms217

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing