6MGL

Crystal structure of the catalytic domain from GH74 enzyme PoGH74 from Paenibacillus odorifer, D60A mutant in complex with XXLG and XGXXLG xyloglucan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CN3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.1 M Tris pH 8.5, 0.2 M magnesium chloride, 25% PEG33530, xyloglucan mixture
Crystal Properties
Matthews coefficientSolvent content
2.2846.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.17α = 90
b = 100.84β = 90
c = 118.689γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9796CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.546.4199.50.0570.0310.70114.54117368
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5394.90.540.3520.70123.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2CN31.546.411.34117296583699.40.150.1480.177RANDOM
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_d13.898
f_angle_d1.098
f_chiral_restr0.069
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5657
Nucleic Acid Atoms
Solvent Atoms1399
Heterogen Atoms232

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building