4PCT

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	0.16 M ammonium sulfate, 16% PEG 6000, 0.1 M imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.61	α = 90
b = 188.83	β = 94.3
c = 97.72	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 2M		2012-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.920	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.1	38.53	93.5	0.119	0.068	7.2	3.6		110866

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	88.8		0.684	0.393	1.8	3.6	5133

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	2wvv	2.1	38.53	110237	5546	92.82	0.2085	0.2066	0.245	RANDOM	32.203

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		-1.76	0.01		-2.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.338
r_dihedral_angle_4_deg	16.92
r_dihedral_angle_3_deg	13.675
r_dihedral_angle_1_deg	5.582
r_mcangle_it	3.715
r_mcbond_it	2.459
r_mcbond_other	2.459
r_angle_refined_deg	1.399
r_angle_other_deg	1.069
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.338
r_dihedral_angle_4_deg	16.92
r_dihedral_angle_3_deg	13.675
r_dihedral_angle_1_deg	5.582
r_mcangle_it	3.715
r_mcbond_it	2.459
r_mcbond_other	2.459
r_angle_refined_deg	1.399
r_angle_other_deg	1.069
r_chiral_restr	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14026
Nucleic Acid Atoms
Solvent Atoms	579
Heterogen Atoms	90

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
PDB_EXTRACT	data extraction
REFMAC	refinement
Aimless	data scaling
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 R01GM133198.