5HDR

Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S,4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291.15	20% PEG3350, 0.1 M ammonium sulfate, 0.1 M imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.5	α = 90
b = 188.76	β = 93.89
c = 98.14	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		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	2.3	67.95	99.7	0.115	0.069	0.992	5.9	3.7		90452

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	2.3	2.34	99.7		1.023	0.616	0.561	1.2	3.7	4527

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	FOURIER SYNTHESIS	THROUGHOUT	2WVV	2.3	97.91	85655	4558	99.39	0.2033	0.2012	0.2435	RANDOM	52.52

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]
4.52		-0.68	-0.07		-4.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.676
r_dihedral_angle_4_deg	19.62
r_dihedral_angle_3_deg	14.653
r_mcangle_it	5.72
r_dihedral_angle_1_deg	5.527
r_mcbond_it	3.882
r_mcbond_other	3.882
r_angle_refined_deg	2.426
r_angle_other_deg	1.555
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.676
r_dihedral_angle_4_deg	19.62
r_dihedral_angle_3_deg	14.653
r_mcangle_it	5.72
r_dihedral_angle_1_deg	5.527
r_mcbond_it	3.882
r_mcbond_other	3.882
r_angle_refined_deg	2.426
r_angle_other_deg	1.555
r_chiral_restr	0.106
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14144
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	153

Software

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

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.