1PT3 | pdb_00001pt3

Crystal structures of nuclease-ColE7 complexed with octamer DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CEI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	298	2.5 mM EDTA, 12.5 mM Tris-HCl (pH 7.5), 0.1 M Ammonium Formate, and 10 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.43	α = 90
b = 46.47	β = 90.39
c = 78.45	γ = 90

Symmetry
Space Group	P 1 21 1

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		2003-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2		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	2.5	40	96.6	0.045	36.4	4.07		15076			32.2

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	2.49	2.58	84.4		0.241	7.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7CEI	2.5	27.73	14389	14389	1455	95.3	0.216	0.216	0.22	0.289	0.29	RANDOM	44.9

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]
5.81		-0.96	9.19		-15

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.4
c_improper_angle_d	4.83
c_scangle_it	3.26
c_mcangle_it	2.46
c_scbond_it	2.08
c_mcbond_it	1.46
c_angle_deg	1.3
c_bond_d	0.011
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	2064
Nucleic Acid Atoms	966
Solvent Atoms	232
Heterogen Atoms

Software

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