4XEG | pdb_00004xeg

Structure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FNC	PDB ENTRY 4FNC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	20% (w/v) PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.199	α = 90
b = 53.393	β = 95.42
c = 82.22	γ = 90

Symmetry
Space Group	C 1 2 1

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 315r		2014-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97948	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.72	39.14	97.2	0.038	0.016	1	23.8	6.6		40036			29.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.75	62.1		0.918	0.491	0.761	1.4	3.8	1332

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4FNC	1.72	39.14	38012	2016	97.1	0.1904	0.1882	0.2	0.2315	0.24	RANDOM	38.544

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]
0.07		-0.03	0.02		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.952
r_dihedral_angle_4_deg	18.905
r_dihedral_angle_3_deg	13.29
r_dihedral_angle_1_deg	6.847
r_mcangle_it	4.258
r_mcbond_it	3.428
r_mcbond_other	3.411
r_angle_refined_deg	1.897
r_angle_other_deg	1.196
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.952
r_dihedral_angle_4_deg	18.905
r_dihedral_angle_3_deg	13.29
r_dihedral_angle_1_deg	6.847
r_mcangle_it	4.258
r_mcbond_it	3.428
r_mcbond_other	3.411
r_angle_refined_deg	1.897
r_angle_other_deg	1.196
r_chiral_restr	0.115
r_bond_refined_d	0.017
r_gen_planes_refined	0.014
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1554
Nucleic Acid Atoms	1135
Solvent Atoms	304
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XDS	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling

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.