3F2Z | pdb_00003f2z

Crystal structure of the C-terminal domain of a chitobiase (BF3579) from Bacteroides fragilis, Northeast Structural Genomics Consortium Target BfR260B

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil	5	277	Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM NaAcetate (pH 5), 40% PEG 8K, and 100 mM NH4Cl , microbatch under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.893	α = 90
b = 51.684	β = 90
c = 63.96	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 4	mirrors	2008-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A		NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.3	30	89.2	0.039	0.044	43.3	5	75798	67612	2	2	9.1

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	1.3	1.35	72.1		0.081	0.089	11.54	2.9	7565

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	1.3	10	2	2	35268	35268	1854	100	0.15628	0.15618	0.1552	0.17	0.17455	0.18	RANDOM	12.287

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]
-0.23			0.38		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.752
r_dihedral_angle_4_deg	16.307
r_dihedral_angle_3_deg	9.438
r_dihedral_angle_1_deg	7.08
r_scangle_it	2.01
r_sphericity_free	1.864
r_sphericity_bonded	1.484
r_scbond_it	1.424
r_angle_refined_deg	1.068
r_mcangle_it	0.987
r_rigid_bond_restr	0.833
r_mcbond_it	0.655
r_nbtor_refined	0.303
r_nbd_refined	0.179
r_symmetry_vdw_refined	0.121
r_xyhbond_nbd_refined	0.096
r_chiral_restr	0.074
r_symmetry_hbond_refined	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1168
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
SOLVE	phasing
RESOLVE	model building
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
RESOLVE	phasing