2IVH

Crystal structure of the nuclease domain of ColE7 (H545Q mutant) in complex with an 18-bp duplex DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8		HANGING DROP VAPOR DIFFUSION METHOD BY MIXING 1 MICRO L COMPLEX SOLUTION AND 1 MICRO L RESERVOIR SOLUTION CONSISTING OF 40 % MPD, 0.4 M AMMONIUM FORMATE AND 0.1 M ACETATE BUFFER (PH4.8) AT ROOM TEMPERATURE., pH 4.80

Crystal Properties
Matthews coefficient	Solvent content
3.53	64.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.8	α = 90
b = 106.8	β = 90
c = 60.2	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	113	CCD	ADSC CCD	MIRRORS	2004-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A		Photon Factory	AR-NW12A

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	2.8	50	99.6	0.08	31.7	10.74		9047			36.2

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	2.8	2.9	99.9		0.36	6.05	11.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PT3	2.8	47.76	8744	919	97.1	0.193	0.193	0.265	RANDOM	45.1

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]
-4.91			-4.91		9.82

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.8
c_scangle_it	11.11
c_scbond_it	8.17
c_mcangle_it	7.52
c_mcbond_it	5.37
c_improper_angle_d	1.17
c_angle_deg	1
c_bond_d	0.006
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	1006
Nucleic Acid Atoms	732
Solvent Atoms	87
Heterogen Atoms	1

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing