3EVY

Crystal structure of a fragment of a putative type I restriction enzyme R protein from Bacteroides fragilis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	20% PEG 3350, 200mM potassium sulfate, pH 7.0, Vapor diffusion, temperature 294K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.834	α = 90
b = 56.47	β = 90
c = 75.857	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		2008-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	1.95	45.314	100	0.114	0.114	9.5	8.4	17791	17791			29.7

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)
	1.95	2.06	100		0.59	0.59	2.6	8.5	2554

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.95	20	17728	17721	900	99.96	0.231	0.229	0.274	RANDOM	45.148

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]
2.91			-0.85		-2.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.75
r_dihedral_angle_4_deg	20.85
r_dihedral_angle_3_deg	16.404
r_scangle_it	5.859
r_dihedral_angle_1_deg	5.04
r_scbond_it	3.8
r_mcangle_it	2.268
r_angle_refined_deg	1.695
r_mcbond_it	1.245
r_chiral_restr	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.75
r_dihedral_angle_4_deg	20.85
r_dihedral_angle_3_deg	16.404
r_scangle_it	5.859
r_dihedral_angle_1_deg	5.04
r_scbond_it	3.8
r_mcangle_it	2.268
r_angle_refined_deg	1.695
r_mcbond_it	1.245
r_chiral_restr	0.132
r_bond_refined_d	0.023
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1402
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	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.