4WSK

Crystal structure of a bacterial fucosidase with phenyl((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)methanone

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JFV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291.15	0.1 M imidazole pH 7.0, 0.2 M ammonium sulfate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.95

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 55.65	�� = 90
b = 186.52	�� = 94.2
c = 98.15	�� = 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		2014-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.92	53.2	96.9	0.102	0.058	0.99	7	4		199312

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	1.92	1.95	96.7		0.909	0.539	0.544	1.8	3.7	7178

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	4JFV	1.92	97.89	139018	7350	96.6	0.1849	0.1824	0.2318	RANDOM	31.583

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]
0.95		-0.75	0.58		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.447
r_dihedral_angle_4_deg	20.794
r_dihedral_angle_3_deg	14.503
r_dihedral_angle_1_deg	6.251
r_mcangle_it	3.834
r_scbond_it	3.637
r_mcbond_it	2.883
r_angle_refined_deg	1.818
r_chiral_restr	0.133
r_bond_refined_d	0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.447
r_dihedral_angle_4_deg	20.794
r_dihedral_angle_3_deg	14.503
r_dihedral_angle_1_deg	6.251
r_mcangle_it	3.834
r_scbond_it	3.637
r_mcbond_it	2.883
r_angle_refined_deg	1.818
r_chiral_restr	0.133
r_bond_refined_d	0.019
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14236
Nucleic Acid Atoms
Solvent Atoms	1204
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

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.