4Z47 | pdb_00004z47

Structure of the enzyme-product complex resulting from TDG action on a GU mismatch in the presence of excess base

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.305	α = 90
b = 53.322	β = 95.31
c = 82.297	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	PIXEL	PSI PILATUS 6M		2014-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	1.00000	SSRL	BL12-2

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	1.45	45.73	94.9	0.068	0.02	0.999	15.9	11.7		64847			27.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47	89.8		0.722	0.645	1.2	11	2991

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	4FNC	1.45	45.73	61716	3110	94.75	0.1428	0.1403	0.15	0.1953	0.2	RANDOM	37.444

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]
1.6		-0.65	-0.28		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.638
r_sphericity_free	29.915
r_sphericity_bonded	18.998
r_dihedral_angle_4_deg	17.134
r_dihedral_angle_3_deg	13.329
r_dihedral_angle_1_deg	6.665
r_mcangle_it	6.399
r_rigid_bond_restr	5.985
r_mcbond_it	4.961
r_mcbond_other	4.938

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.638
r_sphericity_free	29.915
r_sphericity_bonded	18.998
r_dihedral_angle_4_deg	17.134
r_dihedral_angle_3_deg	13.329
r_dihedral_angle_1_deg	6.665
r_mcangle_it	6.399
r_rigid_bond_restr	5.985
r_mcbond_it	4.961
r_mcbond_other	4.938
r_angle_refined_deg	2.274
r_angle_other_deg	1.919
r_chiral_restr	0.151
r_bond_refined_d	0.023
r_gen_planes_refined	0.019
r_gen_planes_other	0.013
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1557
Nucleic Acid Atoms	1135
Solvent Atoms	277
Heterogen Atoms	16

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

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.