2OXM | pdb_00002oxm

Crystal structure of a UNG2/modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping

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	6.5	293	A solution of 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 duplex DNA (2.5 mM)m incubate at room Temperature for 30 min. and then centrifugate at 10000 g for 5 min.Co-crystallizarion condition were 22% PEG 4000, 100 MM HEPES pH 6.5 and 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.467	α = 90
b = 65.567	β = 90
c = 98.472	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	Osmic Mirror	2006-05-11	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	2.5	40	97.1	0.162	8.3	4.1	12024	11434		-3.5	50.583

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	89.4		0.599	0.59	1.91	3.6	1046

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	1EMH	2.5	29.5	12024	11397	535	94.84	0.257	0.257	0.254	0.25	0.328	0.33	RANDOM	39.756

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]
-3.73			-2.92		6.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.169
r_dihedral_angle_3_deg	18.191
r_dihedral_angle_4_deg	11.617
r_dihedral_angle_1_deg	6.268
r_angle_refined_deg	1.712
r_scangle_it	1.675
r_scbond_it	1.025
r_mcangle_it	0.773
r_mcbond_it	0.442
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.169
r_dihedral_angle_3_deg	18.191
r_dihedral_angle_4_deg	11.617
r_dihedral_angle_1_deg	6.268
r_angle_refined_deg	1.712
r_scangle_it	1.675
r_scbond_it	1.025
r_mcangle_it	0.773
r_mcbond_it	0.442
r_nbtor_refined	0.308
r_nbd_refined	0.243
r_symmetry_hbond_refined	0.242
r_symmetry_vdw_refined	0.224
r_xyhbond_nbd_refined	0.208
r_chiral_restr	0.137
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1808
Nucleic Acid Atoms	384
Solvent Atoms	107
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

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.