4PCS | pdb_00004pcs

Crystal structure of a bacterial fucosidase with iminosugar (2S,3S,4R,5S)-3,4-dihydroxy-2-[2'-phenyl]ethynyl-5-methylpyrrolidine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WVV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291.15	0.16 M AS, 14% PEG 6000 0.1 M imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.37	α = 90
b = 188.28	β = 94.1
c = 97.93	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	1.77	39.25	95.9	0.111	0.062	6	4		187759

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	1.77	1.8	96.7		1.72	0.969	0.7	4	9353

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	MOLECULAR REPLACEMENT	THROUGHOUT	2wvv	1.77	39.25	187634	9469	95.75	0.2255	0.2236	0.23	0.2604	0.26	RANDOM	35.533

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]
2.48		-0.62	0.33		-2.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.424
r_dihedral_angle_4_deg	19.002
r_dihedral_angle_3_deg	14.009
r_dihedral_angle_1_deg	5.68
r_mcangle_it	3.832
r_mcbond_it	2.767
r_mcbond_other	2.766
r_angle_refined_deg	1.448
r_angle_other_deg	1.087
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.424
r_dihedral_angle_4_deg	19.002
r_dihedral_angle_3_deg	14.009
r_dihedral_angle_1_deg	5.68
r_mcangle_it	3.832
r_mcbond_it	2.767
r_mcbond_other	2.766
r_angle_refined_deg	1.448
r_angle_other_deg	1.087
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14157
Nucleic Acid Atoms
Solvent Atoms	588
Heterogen Atoms	124

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
PDB_EXTRACT	data extraction
REFMAC	refinement
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 R01GM157729.