2XO6 | pdb_00002xo6

DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XM3	PDB ENTRY 2XM3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.8	292	COMPLEX BUFFER: 35MM TRIS-HCL PH 8.0 0.15M NACL, 10MM MGCL2, 0.5 MM TCEP. PRECIPITATING AGENT: 10MM CDCL2, 0.1M NA-ACETATE PH 4.8, 14% PEG4000. PROTEIN AT 9MG/ML IN COMPLEX BUFFER WAS MIXED WITH LE27 AND T5G. PROTEIN AND DNA OLIGONUCLEOTIDES WERE MIXED IN THE RATIO 1:1.1:1.3. EQUAL VOLUMES OF THIS COMPLEX AND PRECIPITATING AGENT WAS MIXED AT 19 C. CRYOPROTECTION IN 20% V/V GLYCEROL.

Crystal Properties
Matthews coefficient	Solvent content
2.68	53.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.308	α = 90
b = 86.915	β = 90
c = 128.297	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	2008-05-02	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	99.8	0.09	13.4	7.44		44818		-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	99.1		0.19	6.91	4.2

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 2XM3	1.9	30	44616	904	98.8	0.1805	0.1805	0.17	0.2094	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]
2.976			-3.003		0.027

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.9573
c_bond_d	0.018671
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2109
Nucleic Acid Atoms	1338
Solvent Atoms	403
Heterogen Atoms	21

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.