1U78

Structure of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	Na acetate, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.93	77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.681	α = 90
b = 93.681	β = 90
c = 255.558	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2001-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.0749	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.69	12	98.5	0.092	0.092	20		18091	17820			101

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.69	2.8	98.9		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1TC3	2.69	12	18091	17820	954	98.55	0.23515	0.23515	0.23329	0.27291	RANDOM	20.441

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]
-1.94	-0.97		-1.94		2.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.901
r_scangle_it	2.066
r_angle_refined_deg	1.897
r_scbond_it	1.388
r_mcangle_it	1.038
r_mcbond_it	0.557
r_symmetry_hbond_refined	0.246
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.197
r_symmetry_vdw_refined	0.182

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.901
r_scangle_it	2.066
r_angle_refined_deg	1.897
r_scbond_it	1.388
r_mcangle_it	1.038
r_mcbond_it	0.557
r_symmetry_hbond_refined	0.246
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.197
r_symmetry_vdw_refined	0.182
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	816
Nucleic Acid Atoms	1060
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.