4JL2 | pdb_00004jl2

Crystal structure of a bacterial fucosidase with a monovalent iminocyclitol inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4J27	PDB ENTRY 4J27

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291.5	90% dilution of 0.11M AS, 15% PEG6K, 0.1M imidazole pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

Crystal Properties
Matthews coefficient	Solvent content
3	59.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.52	α = 90
b = 95.35	β = 90.13
c = 97.16	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	CCD	MARMOSAIC 225 mm CCD		2011-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.566	97.16	100	0.096	9.7	3.8	135078	135078

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	100		0.541	0.541	1.4	3.8	19645

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 4J27	1.7	97.16	135078	135052	6741	99.92	0.1248	0.1225	0.1372	0.1669	0.177	RANDOM	18.0864

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]
-0.45		-0.35	0.44		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	38.152
r_dihedral_angle_2_deg	32.538
r_dihedral_angle_4_deg	19.993
r_dihedral_angle_3_deg	11.905
r_sphericity_bonded	11.194
r_rigid_bond_restr	10.8
r_dihedral_angle_1_deg	5.658
r_mcangle_it	2.695
r_mcbond_it	2.206
r_mcbond_other	2.206
r_angle_refined_deg	1.337
r_angle_other_deg	0.995
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7051
Nucleic Acid Atoms
Solvent Atoms	1130
Heterogen Atoms	96

Software

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