8BGO

N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus with substrate N,N-diacetylchitobiose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.2M ammonium chloride, 0.1M MES pH6.0, 20% v/v PEG 6000,

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.164	α = 90
b = 151.662	β = 93.33
c = 167.092	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 PILATUS 6M-F		2018-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9797	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.08	48.38	99.3	0.077	14.6	6.7		72565

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.08	3.19	94.75		0.657	2

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	8BGN	3.08	48.38	71565	1000	99.27	0.1687	0.168	0.2147	RANDOM	93.303

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]
-3.11		-2.93	3.19		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.967
r_dihedral_angle_4_deg	16.245
r_dihedral_angle_3_deg	15.468
r_dihedral_angle_1_deg	6.681
r_angle_refined_deg	1.523
r_angle_other_deg	1.199
r_chiral_restr	0.071
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.967
r_dihedral_angle_4_deg	16.245
r_dihedral_angle_3_deg	15.468
r_dihedral_angle_1_deg	6.681
r_angle_refined_deg	1.523
r_angle_other_deg	1.199
r_chiral_restr	0.071
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26314
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	360

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
Coot	model building
PHASER	phasing
REFMAC	refinement

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.