3AIS

Crystal structure of a mutant beta-glucosidase in wheat complexed with DIMBOA-Glc


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229310mM HEPES, 1M LiSO4, 150mM NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
4.7574.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 194.053α = 90
b = 194.053β = 90
c = 194.053γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 42007-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A0.97800Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.2501000.11435.416.263693
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.281000.9833.810.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2DGA2.25058247310796.410.221780.221290.23097RANDOM29.808
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.527
r_dihedral_angle_4_deg21.199
r_dihedral_angle_3_deg13.088
r_scangle_it2.991
r_mcangle_it2.35
r_scbond_it2.066
r_mcbond_it1.542
r_dihedral_angle_1_deg1.461
r_angle_refined_deg1.363
r_nbtor_refined0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.527
r_dihedral_angle_4_deg21.199
r_dihedral_angle_3_deg13.088
r_scangle_it2.991
r_mcangle_it2.35
r_scbond_it2.066
r_mcbond_it1.542
r_dihedral_angle_1_deg1.461
r_angle_refined_deg1.363
r_nbtor_refined0.332
r_nbd_refined0.236
r_symmetry_vdw_refined0.135
r_symmetry_hbond_refined0.132
r_xyhbond_nbd_refined0.127
r_chiral_restr0.104
r_gen_planes_refined0.01
r_bond_refined_d0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3965
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms26

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling