2QF8

Crystal structure of the complex of Buffalo Secretory Glycoprotein with tetrasaccharide at 2.8A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O9O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8298TRIS-HCL, NACL, 19% ETHANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.7355.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.87α = 90
b = 66.499β = 90
c = 107.126γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMirror2007-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.856.850.1434.974.65115681069050.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.90.1434.974.65

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2O9O2.856.81017950892.410.188850.188850.186930.22697RANDOM30.902
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]
-0.87-0.31.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.635
r_scangle_it5.747
r_dihedral_angle_1_deg3.656
r_scbond_it3.497
r_angle_refined_deg2.563
r_mcangle_it2.399
r_mcbond_it1.277
r_nbd_refined0.281
r_symmetry_vdw_refined0.277
r_xyhbond_nbd_refined0.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.635
r_scangle_it5.747
r_dihedral_angle_1_deg3.656
r_scbond_it3.497
r_angle_refined_deg2.563
r_mcangle_it2.399
r_mcbond_it1.277
r_nbd_refined0.281
r_symmetry_vdw_refined0.277
r_xyhbond_nbd_refined0.262
r_symmetry_hbond_refined0.225
r_chiral_restr0.194
r_bond_refined_d0.025
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2894
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing