6T2B

Glycoside hydrolase family 109 from Akkermansia muciniphila in complex with GalNAc and NAD+.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.129215% PEG 2000 MME 0.1 mM sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.1241.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.11α = 90
b = 182.64β = 90.139
c = 70.87γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16MKB mirrors2019-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX1.3799MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.1370.8793.60.99811.617.19233528.91
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.2010.714

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2IXA2.1370.8788157189693.60.15880.1580.193833.22
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_d9.2178
f_angle_d0.7395
f_chiral_restr0.0456
f_plane_restr0.005
f_bond_d0.0039
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13566
Nucleic Acid Atoms
Solvent Atoms1246
Heterogen Atoms262

Software

Software
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing