1RGT

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JY1	PDB structure 1JY1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	PEG 3000, NaCl, HEPES, spermine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.791	α = 90
b = 104.894	β = 90
c = 194.124	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	100	CCD	ADSC QUANTUM 4		2003-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9791	ALS	8.2.2

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	50	97.4	0.085	15.29	4.15		68032		-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)
	2	2.07	91.2		0.368	3.38

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	MIR	THROUGHOUT	PDB structure 1JY1	2	50	67981	64557	3424	97.46	0.19595	0.19595	0.19428	0.22761	RANDOM	23.713

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]
-1.4			2.7		-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.157
r_scangle_it	3.745
r_scbond_it	2.481
r_mcangle_it	2.382
r_mcbond_it	1.457
r_angle_refined_deg	1.161
r_angle_other_deg	0.762
r_nbd_other	0.437
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.209

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.157
r_scangle_it	3.745
r_scbond_it	2.481
r_mcangle_it	2.382
r_mcbond_it	1.457
r_angle_refined_deg	1.161
r_angle_other_deg	0.762
r_nbd_other	0.437
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.209
r_nbtor_other	0.192
r_symmetry_hbond_refined	0.183
r_xyhbond_nbd_refined	0.176
r_metal_ion_refined	0.109
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6827
Nucleic Acid Atoms	100
Solvent Atoms	222
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	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.