4B9Z

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with Acarbose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B9YPDB ENTRY 4B9Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH7.0), 2% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.1160.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.88α = 90
b = 196.88β = 90
c = 102.76γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
1251.381000.1122.221.57907824.58
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)
122.11000.467.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4B9Y249.7341.9179078397499.970.1620.16070.1874
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]
-3.2253-3.22536.4505
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.909
f_angle_d1.094
f_chiral_restr0.078
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6203
Nucleic Acid Atoms
Solvent Atoms444
Heterogen Atoms142

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing