3ECP | pdb_00003ecp

Crystal Structure Of Tn5 Transposase Complexed With 5' Phosphorylated Transposon End DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MUH	PDB ENTRY 1MUH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	293	13% (w/v) oMe-PEG 5000, 0.1M bis-tris, 0.1M ammonium sulfate, pH 6.5, microbatch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.508	α = 90
b = 113.508	β = 90
c = 228.775	γ = 120

Symmetry
Space Group	P 65 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	CCD	ADSC QUANTUM 315		2006-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.00964	APS	19-ID

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	2.5	30	100	0.044	69.5	20.4	31006	30992			66.4

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	2.5	2.59	100		0.379	9	18	3032

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 (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 1MUH	2.5	30	29364	29291	1556	99.75	0.22153	0.22153	0.21878	0.24	0.27386	0.29	RANDOM	61.752

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]
-1.87	-0.94		-1.87		2.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.275
r_dihedral_angle_3_deg	17.216
r_dihedral_angle_4_deg	12.304
r_dihedral_angle_1_deg	5.978
r_scangle_it	4.256
r_mcangle_it	3.649
r_scbond_it	3.504
r_mcbond_it	2.498
r_angle_refined_deg	1.529
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.275
r_dihedral_angle_3_deg	17.216
r_dihedral_angle_4_deg	12.304
r_dihedral_angle_1_deg	5.978
r_scangle_it	4.256
r_mcangle_it	3.649
r_scbond_it	3.504
r_mcbond_it	2.498
r_angle_refined_deg	1.529
r_nbtor_refined	0.308
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.182
r_xyhbond_nbd_refined	0.159
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3605
Nucleic Acid Atoms	818
Solvent Atoms	120
Heterogen Atoms	18

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.