4PEE | pdb_00004pee

Crystal structure of a bacterial fucosidase with inhibitor 1-phenyl-4-[(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-yl]triazole

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	7	291.15	20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.04	α = 90
b = 187.59	β = 94.26
c = 97.7	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-F		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)	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	1.95	55.89	98.2	0.081	0.047	8.8	3.9		143082

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	1.95	1.98	97.4		0.827	0.474	1.7	3.9	7014

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	AB INITIO PHASING	THROUGHOUT	4JFV	1.95	97.43	143017	7202	98.06	0.1926	0.1907	0.2	0.229	0.23	RANDOM	37.86

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]
2.28		-1.07	-0.95		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.535
r_dihedral_angle_4_deg	16.583
r_dihedral_angle_3_deg	13.844
r_dihedral_angle_1_deg	5.804
r_mcangle_it	4.384
r_mcbond_it	3.317
r_mcbond_other	3.314
r_angle_refined_deg	1.53
r_angle_other_deg	1.254
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.535
r_dihedral_angle_4_deg	16.583
r_dihedral_angle_3_deg	13.844
r_dihedral_angle_1_deg	5.804
r_mcangle_it	4.384
r_mcbond_it	3.317
r_mcbond_other	3.314
r_angle_refined_deg	1.53
r_angle_other_deg	1.254
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14284
Nucleic Acid Atoms
Solvent Atoms	892
Heterogen Atoms	136

Software

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

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.