6S04 | pdb_00006s04

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-glycolylneuraminic 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	0.8 M sodium formate, 12% PEG 4000, 0.1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.053	α = 90
b = 79.548	β = 94.95
c = 113.52	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 EIGER X 16M		2019-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2	65.07	100	0.236	0.269	0.126	0.963	3.7	4.1		78077

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	2.04	100		0.635	0.723	0.342	0.739		4.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6RZD	2	64.89	74113	3941	99.94	0.2317	0.2294	0.24	0.2763	0.28	RANDOM	17.122

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]
1.1		-0.45	-0.14		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.578
r_dihedral_angle_4_deg	21.162
r_dihedral_angle_3_deg	14.666
r_dihedral_angle_1_deg	7.702
r_angle_refined_deg	1.881
r_angle_other_deg	1.278
r_chiral_restr	0.085
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	29.578
r_dihedral_angle_4_deg	21.162
r_dihedral_angle_3_deg	14.666
r_dihedral_angle_1_deg	7.702
r_angle_refined_deg	1.881
r_angle_other_deg	1.278
r_chiral_restr	0.085
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	8023
Nucleic Acid Atoms
Solvent Atoms	550
Heterogen Atoms	84

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.