6S0E

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-Acetyl-2,3-dehydro-2-deoxyneuraminic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RZD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.2 M potassium bromide, 15% PEG 4000, 0.1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.418	α = 90
b = 78.756	β = 94.96
c = 112.82	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 PILATUS3 S 6M		2018-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	1.9	78.76	99.9	0.17	0.198	0.099	0.91	5	4		87227

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	1.9	1.93	99.9		0.553	0.655	0.342	0.756		3.8

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	6RZD	1.9	64.58	82866	4328	99.87	0.2531	0.2504	0.3067	RANDOM	20.945

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]
2.69		0.04	-1.05		-1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.063
r_dihedral_angle_4_deg	19.733
r_dihedral_angle_3_deg	15.4
r_dihedral_angle_1_deg	7.626
r_angle_refined_deg	1.841
r_angle_other_deg	1.319
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.063
r_dihedral_angle_4_deg	19.733
r_dihedral_angle_3_deg	15.4
r_dihedral_angle_1_deg	7.626
r_angle_refined_deg	1.841
r_angle_other_deg	1.319
r_chiral_restr	0.083
r_bond_refined_d	0.012
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	8020
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	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 R01GM157729.