2RBA

Structure of Human Thymine DNA Glycosylase Bound to Abasic and Undamaged DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WYW	PDB ENTRY 1wyw, SUMO removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	8 mg/ml protein and 20% molar excess DNA duplex in 10mM Tris-HCL, 100 mM NaCl, 0.5mM DTT. Reservoir: 20% PEG 3350, 0.2M K/Na tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.133	α = 90
b = 162.133	β = 90
c = 56.142	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	CCD	ADSC QUANTUM 315		2007-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.91837	SSRL	BL9-1

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	2.79	50	99.6	0.083	0.083	25.5	10.4	21137	21137			87.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.89	96.8		1	7.9	2031

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1wyw, SUMO removed	2.79	50	19458	1048	97.49	0.23211	0.22965	0.27629	RANDOM	110.074

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]
-4.52	-2.26		-4.52		6.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.864
r_dihedral_angle_4_deg	24.614
r_dihedral_angle_3_deg	22.542
r_dihedral_angle_1_deg	9.62
r_scangle_it	2.984
r_angle_refined_deg	2.272
r_scbond_it	1.839
r_mcangle_it	1.66
r_mcbond_it	0.978
r_nbtor_refined	0.338
r_nbd_refined	0.29
r_symmetry_vdw_refined	0.289
r_symmetry_hbond_refined	0.246
r_xyhbond_nbd_refined	0.208
r_chiral_restr	0.17
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2916
Nucleic Acid Atoms	929
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing