Experiment: 7VI6

Crystal structure of GH3 beta-N-acetylhexosaminidase Amuc_2109 from Akkermansia muciniphila

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZM6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	2M NaCl, 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.926	α = 90
b = 81.105	β = 90
c = 126.991	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M		2020-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NFPSS BEAMLINE BL19U1	0.9785	NFPSS	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	50	99.8	0.123	0.136	0.056	6.3	6.3		55774

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)	Redundancy	Number Unique Reflections (All)
1	2	2.07	100		0.881	0.959	0.375	0.87		6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	THROUGHOUT	4ZM6	2	39.46	1.34	55624	2776	99.67	0.1855	0.1834	0.1881	0.2255	0.2232	43.0295

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5203
Nucleic Acid Atoms
Solvent Atoms	500
Heterogen Atoms	15

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing