1ZNV

How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MZ8	PDB ENTRY 1MZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	298	0.3M phosphate buffer, 50mM NaCl, 20% PEG550 MME, 10% glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.021	α = 90
b = 62.882	β = 90
c = 74.769	γ = 90

Symmetry
Space Group	P 21 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	120	CCD	ADSC QUANTUM 4		2004-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	1.0	SPring-8	BL12B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2	40	99.8	0.082	25.34	5.8	224307	223845			16.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07			0.381	5.73		4763

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	Isomorphous to 1MZ8	THROUGHOUT	PDB ENTRY 1MZ8	2	27.65	38658	37511	3023	96.9	0.188	0.188	0.235	RANDOM	32.8

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]
-9.19			9.56		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21
c_scangle_it	7.42
c_scbond_it	5.25
c_mcangle_it	4.31
c_mcbond_it	3.32
c_angle_deg	1.3
c_improper_angle_d	0.84
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3328
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
CNS	phasing