2XQC | pdb_00002xqc

DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE AND ZN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XO6	PDB ENTRY 2XO6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	292	COMPLEX BUFFER: 35MM TRIS-HCL PH8.0, 0.15M NACL, 10MM MGCL2, 0.5 MM TCEP. THE TERNARY COMPLEX WAS FORMED BY MIXING PROTEIN AT 9MG/ML WITH THE LE BINDING SITE DNA AND CLEAVAGE SITE DNA AT A RATIO OF 1:1.1:1.3 CRYSTALS WERE OBTAINED AT 19C BY MIXING THE COMPLEX AT 1:1 WITH WELL SOLUTION OF 10MM ZNCL2, 0.1M NA-ACETATE PH 4.2, 17& PEG 4000. CRYSTALS WERE CRYOPROTECTED IN 20% GLYCEROL.

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.762	α = 90
b = 92.716	β = 90
c = 126.07	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	IMAGE PLATE	RIGAKU RAXIS IV	MULTILAYER MIRRORS	1998-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	1.9	30	96.7	0.05	16.4	7.24		45279		-3

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	1.9	1.95	75.9		0.24	4.49	2.4

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 2XO6	1.9	30	44429	900	94.9	0.1758	0.1758	0.17	0.2089	0.2	RANDOM

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]
-4.189			4.103		0.086

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	4.8032
c_bond_d	0.012338
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
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2106
Nucleic Acid Atoms	1338
Solvent Atoms	474
Heterogen Atoms	9

Software

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