X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSambucus nigra agglutinin II (SNA-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
2.6954.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.042α = 90
b = 127.042β = 90
c = 75.492γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.445.4199.50.0690.06917.66.3601756017515.2
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)
11.41.4498.40.180.186.44.24332

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 (SNA-II) tetragonal crystal form1.4205704857048303899.250.143270.143270.140950.1873RANDOM13.791
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]
0.060.06-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.271
r_dihedral_angle_4_deg22.053
r_dihedral_angle_3_deg11.655
r_sphericity_free10.285
r_scangle_it7.227
r_dihedral_angle_1_deg7.173
r_scbond_it5.624
r_sphericity_bonded5.198
r_mcangle_it4.552
r_mcbond_it3.951
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.271
r_dihedral_angle_4_deg22.053
r_dihedral_angle_3_deg11.655
r_sphericity_free10.285
r_scangle_it7.227
r_dihedral_angle_1_deg7.173
r_scbond_it5.624
r_sphericity_bonded5.198
r_mcangle_it4.552
r_mcbond_it3.951
r_rigid_bond_restr2.757
r_mcbond_other2.751
r_angle_refined_deg1.922
r_angle_other_deg1.054
r_symmetry_vdw_other0.307
r_symmetry_hbond_refined0.233
r_nbd_refined0.227
r_nbd_other0.218
r_symmetry_vdw_refined0.209
r_xyhbond_nbd_refined0.194
r_nbtor_refined0.172
r_chiral_restr0.127
r_nbtor_other0.117
r_bond_refined_d0.021
r_gen_planes_refined0.011
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 Atoms339
Heterogen Atoms163

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing