4ZOA

Crystal Structure of beta-glucosidase from Listeria innocua in complex with isofagomine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZOE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298PEG 4000, NaCl, LiSO4, glycerol
Crystal Properties
Matthews coefficientSolvent content
2.8657.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.65α = 90
b = 94.85β = 96.2
c = 215.868γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102013-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1741.4998.37.13.292779

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 REPLACEMENTTHROUGHOUT4ZOE2.1740.7188062463897.580.19470.19140.2578RANDOM20.178
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]
0.03-0.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_4_deg23.21
r_sphericity_free15.357
r_dihedral_angle_3_deg15.104
r_dihedral_angle_1_deg6.786
r_sphericity_bonded5.03
r_rigid_bond_restr3.646
r_angle_other_deg2.129
r_angle_refined_deg1.791
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_4_deg23.21
r_sphericity_free15.357
r_dihedral_angle_3_deg15.104
r_dihedral_angle_1_deg6.786
r_sphericity_bonded5.03
r_rigid_bond_restr3.646
r_angle_other_deg2.129
r_angle_refined_deg1.791
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_gen_planes_other0.008
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11063
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms29

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction