1Y2X

Crystal structure of the tetragonal form of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen and N-acetylglucosamine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298PEG 8000, lithium sulfate, isopropanol, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.766.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.675α = 90
b = 85.675β = 90
c = 257.073γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHSilicon toroidal mirror coated with Rhodium2004-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.923ESRFID23-1

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
12.353099.70.0795.57.94025940259
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)
12.362.4498.60.1673.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSTRUCTURE OF UNLIGANDED LECTIN2.36303838038380202899.780.228810.228810.227560.25241RANDOM26.169
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]
0.440.44-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.167
r_scangle_it1.853
r_angle_refined_deg1.215
r_scbond_it1.144
r_mcangle_it0.732
r_mcbond_it0.373
r_nbd_refined0.177
r_symmetry_hbond_refined0.142
r_symmetry_vdw_refined0.127
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.167
r_scangle_it1.853
r_angle_refined_deg1.215
r_scbond_it1.144
r_mcangle_it0.732
r_mcbond_it0.373
r_nbd_refined0.177
r_symmetry_hbond_refined0.142
r_symmetry_vdw_refined0.127
r_chiral_restr0.116
r_xyhbond_nbd_refined0.098
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4540
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing