1RFF

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JY1	PDB entry 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
2.23	44.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.076	α = 90
b = 104.904	β = 90
c = 193.832	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	1.00	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	1.7	50	90.6	0.071	21.04	4.52	103225	103255		-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)
	1.7	1.76	64.6		0.482	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	PDB entry 1jy1	1.7	50	102833	97672	5161	90.78	0.19364	0.19364	0.19258	0.21325	RANDOM	24.569

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]
-0.63			2		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.254
r_scangle_it	4.29
r_scbond_it	2.824
r_mcangle_it	2.754
r_mcbond_it	1.745
r_angle_refined_deg	1.335
r_symmetry_vdw_refined	0.211
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.254
r_scangle_it	4.29
r_scbond_it	2.824
r_mcangle_it	2.754
r_mcbond_it	1.745
r_angle_refined_deg	1.335
r_symmetry_vdw_refined	0.211
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.102
r_metal_ion_refined	0.1
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6933
Nucleic Acid Atoms	102
Solvent Atoms	343
Heterogen Atoms	34

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.