2VJV | pdb_00002vjv

Crystal structure of the IS608 transposase in complex with left end 26-mer DNA hairpin and a 6-mer DNA representing the left end cleavage site

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		6-10% PEG 600 AND 50 MM SODIUM CITRATE PH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.29	50.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.292	α = 90
b = 72.407	β = 90
c = 110.174	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 IMAGE PLATE	MULTILAYER FOCUSING OPTICS	2007-06-12	M	SINGLE WAVELENGTH

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

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	40	89.8	0.15	11.3	3.9		38044			17.3

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	64.2		0.27	4.6	1.9

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 2VIH	1.9	24.61	37220	1131	87.8	0.194	0.194	0.19	0.227	0.22	RANDOM	29.6

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]
-1.66			1.98		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25
c_scbond_it	9.78
c_scangle_it	8.98
c_angle_deg	3.6
c_mcangle_it	3.01
c_mcbond_it	1.76
c_improper_angle_d	1.39
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2046
Nucleic Acid Atoms	1298
Solvent Atoms	275
Heterogen Atoms	3

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.