2XMA | pdb_00002xma

DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE RIGHT END DNA COMPLEX

X-RAY DIFFRACTION

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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		8		COMLEX BUFFER: 35MM TRIS-HCL PH 8.O, 0.1 M NA-MALONATE 10MM MGCL2M 0.5 MM TCEP PRECIPITATING AGENT: 0.16 MM MGCL2, 0.1 M TRIS-HCL PH 7.9, 3.4M 1,6-HEXANEDIOL FROZEN IN LIQUID PROPANE W/O ADDITIONAL CRYOPROTECTION

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.827	α = 90
b = 89.288	β = 111.23
c = 90.104	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	95	IMAGE PLATE	RIGAKU RAXIS IV	MULTI-LAYER MIRRORS	2008-03-17	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 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	2.3	30	99.6	0.05	16.4	3.62		50130		-3

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	2.3	2.37	99		0.39	3.09	3.2

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	2.3	30	47910	953	94.9	0.2152	0.2152	0.21	0.2375	0.23	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]
-3.051		4.602	-1.034		4.085

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	2.77184
c_bond_d	0.005776
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	4458
Nucleic Acid Atoms	2778
Solvent Atoms	229
Heterogen Atoms	4

Software

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