Experiment: 6T2B

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IXA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	292	15% PEG 2000 MME 0.1 mM sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.91

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	KB mirrors	2019-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	1.3799	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.13	70.87	93.6	0.998	11.61	7.1		92335			28.91

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.201			0.714

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2IXA	2.13	70.87	88157	1896	93.6	0.1588	0.158	0.1589	0.1938	0.194	33.22

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.2178
f_angle_d	0.7395
f_chiral_restr	0.0456
f_plane_restr	0.005
f_bond_d	0.0039

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13566
Nucleic Acid Atoms
Solvent Atoms	1246
Heterogen Atoms	262

Software

Software
Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
Coot	model building
PHASER	phasing