2X42

Structure of beta-glucosidase 3B from Thermotoga neapolitana in complex with alpha-D-glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X40PDB ENTRY 2X40

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.42933-5 MG/ML PROTEIN, 16-18 % (V/V) PEG 3350, 0.2 M NABR, 90 MM BIS-TRIS PROPANE PH 7.4, 20C
Crystal Properties
Matthews coefficientSolvent content
2.5757

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.55α = 90
b = 128.16β = 90
c = 175.65γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-165MULTILAYER MIRRORS2008-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

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
12.129.296.50.0715.44.64770632.69
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)
12.12.278.30.562.2

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 2X402.09929.2751.3547687240296.340.17370.17150.213536.8
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
f_dihedral_angle_d15.793
f_angle_d0.883
f_chiral_restr0.063
f_bond_d0.005
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5676
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms16

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
PHENIXphasing
PHENIXrefinement