3UFB | pdb_00003ufb

Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	20 % (w/v) polyethylene glycol 8,000, 0.1 M at Hepes pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
2	VAPOR DIFFUSION, HANGING DROP	7.5	291	24 % (w/v) polyethyleneglycol 3350, 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid at pH 7.5 and 10 mM -mercaptoethanol , VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.899	α = 90
b = 78.899	β = 90
c = 165.802	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315r		2008-11-12	M	SINGLE WAVELENGTH
2	2	x-ray		CCD	ADSC QUANTUM 315r		2011-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.0	PAL/PLS	4A
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.98962	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	50	99.9				48972	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	1.8	5.999	0.1	47581	4811	99.46	0.1844	0.1809	0.18	0.2154	0.21	29.2993

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]
-2.9082			-2.9082		5.8163

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.761
f_angle_d	1.006
f_chiral_restr	0.069
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3856
Nucleic Acid Atoms
Solvent Atoms	542
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.