3CEW | pdb_00003cew

Crystal structure of a cupin protein (BF4112) from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR205

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	6	277	Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Precipitant solution: 100 mM MES pH 6.0, 20% PEG 4000, 100 mM Magnesium chloride, MICROBATCH UNDER OIL, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.14	α = 90
b = 87.834	β = 90
c = 128.032	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	MAR CCD 165 mm	Mirrors	2008-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97900	NSLS	X4C

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	2.3	30	94.3	0.074	0.073	30.36	7.5	43936	43936			17.1

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	2.3	2.38	100		0.134	0.124	13.38	7.7	4634

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.31	19.81	2	43936	41989	4094	89.8	0.218	0.217	0.217	0.2297	0.246	0.2567	RANDOM	21.2

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]
1.14			-1.01		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.4
c_angle_deg	1.3
c_improper_angle_d	0.71
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3552
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing

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.