Experiment: 2OYT

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	Recombinat human UNG2 (22 mg/ml) in 50 mM tris-OAc buffer pH 7.0, 150 mM NaCl and 1mM DTT was mixed with T/M DNA duplex (2.5 mM) inclubate at room T for 30 min and then centrifugate at 10000 g for 5 min. Co-crystallization conditions 22-25% PEG 4000, 10mM Hepes pH 6.5, 1mM DTT, 0.5 % v/v dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.499	α = 90
b = 66.318	β = 90
c = 100.316	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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	36.47	90.4	0.066	43.7	5.8		20504			29.9

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	2	2.07	55.4		0.247	6.36	3.6

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 (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	1EMH	2	36.47	20446	1019	90.74	0.194	0.194	0.192	0.19	0.238	0.24	RANDOM	28.728

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]
-2.01			0.72		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.605
r_dihedral_angle_3_deg	12.376
r_dihedral_angle_1_deg	5.172
r_dihedral_angle_4_deg	3.85
r_scangle_it	1.241
r_angle_refined_deg	1.209
r_scbond_it	0.777
r_mcangle_it	0.592
r_mcbond_it	0.353
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.605
r_dihedral_angle_3_deg	12.376
r_dihedral_angle_1_deg	5.172
r_dihedral_angle_4_deg	3.85
r_scangle_it	1.241
r_angle_refined_deg	1.209
r_scbond_it	0.777
r_mcangle_it	0.592
r_mcbond_it	0.353
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.242
r_nbd_refined	0.17
r_symmetry_hbond_refined	0.12
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1808
Nucleic Acid Atoms	376
Solvent Atoms	398
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	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.