7F7R

Enterococcus faecalis GH31 alpha-N-acetylgalactosaminidase D455N in complex with Tn antigen

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	25% PEG3350, 0.2 M ammonium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.706	α = 90
b = 82.973	β = 90
c = 148.58	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 PILATUS3 S 2M		2020-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.63	50	100	0.068	0.07	0.019	1	23.8	13.1		127951

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)	Redundancy	Number Unique Reflections (All)
1	1.63	1.72	100		0.961	0.287	0.809	2.6	12.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6M76	1.63	46.04	127854	6325	99.986	0.178	0.1772	0.2004	27.096

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]
2.041			-2.18		0.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.327
r_dihedral_angle_4_deg	19.223
r_dihedral_angle_3_deg	13.187
r_dihedral_angle_1_deg	7.276
r_lrange_it	4.622
r_lrange_other	4.563
r_scangle_it	2.343
r_scangle_other	2.343
r_angle_refined_deg	1.629
r_mcangle_other	1.615
r_mcangle_it	1.614
r_scbond_it	1.5
r_scbond_other	1.5
r_angle_other_deg	1.435
r_mcbond_it	1.035
r_mcbond_other	1.031
r_nbd_refined	0.206
r_symmetry_nbd_refined	0.196
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.152
r_nbd_other	0.131
r_metal_ion_refined	0.122
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7036
Nucleic Acid Atoms
Solvent Atoms	558
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building