6N1B

Crystal structure of an N-acetylgalactosamine deacetylase from F. plautii in complex with blood group B trisaccharide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M CaCl2, 0.1 M MES pH 6.0, 18% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.68	26.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.71	α = 90
b = 69.24	β = 90
c = 104.81	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 6M		2018-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.979	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.3	46.4	97.3	0.024	1	16.3	5.5		90596

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	69.1		0.259	0.76	1.9	1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6N1A	1.3	46.4	86066	4530	97.19	0.1473	0.1465	0.1621	RANDOM	13.372

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]
-0.31			-0.4		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.885
r_dihedral_angle_4_deg	14.482
r_dihedral_angle_3_deg	12.515
r_dihedral_angle_1_deg	7.616
r_angle_other_deg	3.887
r_angle_refined_deg	2.227
r_mcangle_it	1.814
r_mcbond_it	1.331
r_mcbond_other	1.317
r_chiral_restr	0.167

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.885
r_dihedral_angle_4_deg	14.482
r_dihedral_angle_3_deg	12.515
r_dihedral_angle_1_deg	7.616
r_angle_other_deg	3.887
r_angle_refined_deg	2.227
r_mcangle_it	1.814
r_mcbond_it	1.331
r_mcbond_other	1.317
r_chiral_restr	0.167
r_bond_refined_d	0.027
r_gen_planes_other	0.026
r_gen_planes_refined	0.015
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3061
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.