2JBG | pdb_00002jbg

crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7

X-RAY DIFFRACTION

---

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		4.6		20 % W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, 0.2 M AMMONIUM SULFATE, AND 0.1 M SODIUM ACETATE TRIHYDRATE AT PH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.18	α = 90
b = 62.683	β = 90
c = 74.785	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	113	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2004-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	2.2	37.4	99.9	0.07	27.1	6.7		29109			18.1

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	2.28	100		0.38	5.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1MZ8	2.2	37.4	28439	2831	97.5	0.202	0.202	0.2	0.249	0.24	RANDOM	31.7

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]
-4.09			1.02		3.08

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.8
c_scangle_it	3.49
c_scbond_it	2.37
c_mcangle_it	2.16
c_mcbond_it	1.35
c_angle_deg	1.1
c_improper_angle_d	0.83
c_bond_d	0.007
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	3350
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	12

Software

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