5I5R

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MNZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291.15	20% w/v PEG 3350, 0.1 M ammonium sulfate, 0.1 M imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.08	α = 90
b = 187.699	β = 94.21
c = 97.64	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 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)	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	2.1	67.57	99.8	0.096	0.992	6.8	3.8		116721

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	99.8		0.891		3.9

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	1MNZ	2.1	67.57	110778	5869	99.75	0.1971	0.1951	0.2361	RANDOM	44.105

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]
2.23		-1.15	0.17		-2.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.431
r_dihedral_angle_4_deg	19.149
r_dihedral_angle_3_deg	14.116
r_dihedral_angle_1_deg	5.793
r_mcangle_it	5.085
r_mcbond_it	3.681
r_mcbond_other	3.679
r_angle_refined_deg	1.505
r_angle_other_deg	1.319
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.008
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14201
Nucleic Acid Atoms
Solvent Atoms	773
Heterogen Atoms	140

Software

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