X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSAMBUCUS NIGRA AGGLUTININ ii 6 TETRGONAL 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
11.5534.6898.80.0440.04432.45.7435014350115.4
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)
11.551.6492.90.0950.09511.53.25890

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 6 TETRGONAL CRYSTAL FORM1.55204127641276218698.760.124850.124850.122650.16707RANDOM12.673
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]
-0.13-0.130.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.971
r_dihedral_angle_4_deg19.88
r_dihedral_angle_3_deg11.935
r_sphericity_free11.584
r_dihedral_angle_1_deg7.2
r_scangle_it5.782
r_sphericity_bonded4.584
r_scbond_it4.286
r_mcangle_it2.776
r_mcbond_it2.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.971
r_dihedral_angle_4_deg19.88
r_dihedral_angle_3_deg11.935
r_sphericity_free11.584
r_dihedral_angle_1_deg7.2
r_scangle_it5.782
r_sphericity_bonded4.584
r_scbond_it4.286
r_mcangle_it2.776
r_mcbond_it2.261
r_rigid_bond_restr2.124
r_angle_refined_deg2.026
r_angle_other_deg1.072
r_mcbond_other0.845
r_symmetry_vdw_other0.342
r_symmetry_vdw_refined0.28
r_symmetry_hbond_refined0.267
r_nbd_refined0.233
r_xyhbond_nbd_refined0.225
r_nbd_other0.213
r_nbtor_refined0.17
r_chiral_restr0.16
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 Atoms1978
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing