4M81

The structure of E292S glycosynthase variant of exo-1,3-beta-glucanase from Candida albicans complexed with 1-fluoro-alpha-D-glucopyranoside (donor) and p-nitrophenyl beta-D-glucopyranoside (acceptor) at 1.86A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CZ1pdb entry 1CZ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.32910.1M HEPES-KOH, 0.2M CACL2, 19% PEG8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9737.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.006α = 90
b = 64.202β = 90
c = 95.037γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATEMAR scanner 345 mm plate2004-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.8637.0190.70.0880.08815.55.2283172824917.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.96740.5270.5272.73.93304

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1CZ11.8618.0921.342824928109139890.130.15150.14850.2106RANDOM
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_d13.662
f_angle_d1.041
f_chiral_restr0.075
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3211
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms39

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling