3BS3

Crystal structure of a putative DNA-binding protein from Bacteroides fragilis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	0.1M Tris-HCl pH 8.5, 0.2M LiSO4, 1.25M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.337	α = 90
b = 63.337	β = 90
c = 34.706	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	ADSC QUANTUM 315		2007-11-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97931, 0.97945	APS	19-ID

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	1.65	50	98	0.094	9.2	11.9	9728	9728		-3	26.1

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	1.65	1.69	98		0.509	2.9	10	632

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.65	29.32	9714	9714	463	98.02	0.185	0.185	0.183	0.219	RANDOM	32.059

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]
-1.1	-0.55		-1.1		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.062
r_dihedral_angle_4_deg	16.164
r_dihedral_angle_3_deg	14.635
r_dihedral_angle_1_deg	4.079
r_scangle_it	3.348
r_scbond_it	2.266
r_mcangle_it	1.355
r_angle_refined_deg	1.346
r_mcbond_it	0.989
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.062
r_dihedral_angle_4_deg	16.164
r_dihedral_angle_3_deg	14.635
r_dihedral_angle_1_deg	4.079
r_scangle_it	3.348
r_scbond_it	2.266
r_mcangle_it	1.355
r_angle_refined_deg	1.346
r_mcbond_it	0.989
r_nbtor_refined	0.305
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.207
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	502
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	9

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

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.