3RWX

Crystal structure of a putative outer membrane protein (BF2706) from Bacteroides fragilis NCTC 9343 at 2.40 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	0.2M potassium sodium tartrate, 2.0M ammonium sulfate, 0.1M sodium citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.81	74.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.154	α = 90
b = 154.154	β = 90
c = 40.164	γ = 120

Symmetry
Space Group	P 31 2 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 325 mm CCD	Vertical focusing mirror; double crystal Si(111) monochromator	2011-03-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.96109,0.97934,0.97908	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	29.816	98.4	0.09	10.91			21589		-3	48.034

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	96.7		0.672	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.4	29.816	21577	1107	99.78	0.2006	0.1984	0.2418	RANDOM	33.2552

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]
1.09	0.54		1.09		-1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.691
r_dihedral_angle_3_deg	13.986
r_dihedral_angle_4_deg	9.802
r_dihedral_angle_1_deg	5.967
r_scangle_it	3.924
r_scbond_it	2.266
r_angle_refined_deg	1.518
r_mcangle_it	1.316
r_angle_other_deg	0.83
r_mcbond_it	0.638

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.691
r_dihedral_angle_3_deg	13.986
r_dihedral_angle_4_deg	9.802
r_dihedral_angle_1_deg	5.967
r_scangle_it	3.924
r_scbond_it	2.266
r_angle_refined_deg	1.518
r_mcangle_it	1.316
r_angle_other_deg	0.83
r_mcbond_it	0.638
r_mcbond_other	0.119
r_chiral_restr	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1928
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	52

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	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 R01GM133198.