6XQF

Crystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with 1,3-beta-D-cellotriosyl-glucose, presenting a 1,3-beta-D-cellobiosyl-glucose at active site


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529130 % PEG4000, 0.2 M magnesium chloride, and 0.1 M Tris
Crystal Properties
Matthews coefficientSolvent content
1.8533.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.692α = 90
b = 49.868β = 90
c = 114.474γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4583LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.5845.7297.20.0840.0940.0420.98913.9530357
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6177.70.3670.4470.2470.6312.9

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 REPLACEMENTTHROUGHOUT6XOF1.5845.7228544148796.260.17330.17140.2089RANDOM10.568
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]
-0.60.10.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.913
r_dihedral_angle_4_deg16.066
r_dihedral_angle_3_deg11.91
r_dihedral_angle_1_deg8.093
r_angle_refined_deg1.941
r_angle_other_deg1.554
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.913
r_dihedral_angle_4_deg16.066
r_dihedral_angle_3_deg11.91
r_dihedral_angle_1_deg8.093
r_angle_refined_deg1.941
r_angle_other_deg1.554
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2023
Nucleic Acid Atoms
Solvent Atoms455
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction