3ZI5 | pdb_00003zi5

Crystal STRUCTURE OF RESTRICTION ENDONUCLEASE BFII C-TERMINAL RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C1L	PDB ENTRY 2C1L CHAIN A RESIDUES 200-358

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			292	CRYSTALS WERE GROWN AT 19C BY MIXING COMPLEX SOLUTION WITH THE CRYSTALLIZATION BUFFER 0.49 M NAH2PO4, 0.91 M K2HPO4 (PH6.9 AT 25C).

Crystal Properties
Matthews coefficient	Solvent content
2.41	58.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.18	α = 90
b = 175.18	β = 90
c = 35.789	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	287	IMAGE PLATE	RIGAKU IMAGE PLATE	OSMIC CONFOCAL MIRRORS	2009-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	3.2	50.57	100	0.15	13.31	6.97		10809		3	24.38

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	3.2	3.23	100		0.24	5.43	6.49

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	MOLECULAR REPLACEMENT	PDB ENTRY 2C1L CHAIN A RESIDUES 200-358	3.2	43.795	1.35	10790	1040	99.93	0.1805	0.1757	0.18	0.2259	0.22

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.882
f_angle_d	0.743
f_chiral_restr	0.029
f_bond_d	0.003
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2642
Nucleic Acid Atoms	972
Solvent Atoms	28
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
TRUNCATE	data scaling
MOLREP	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.