4LYL

Crystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the proteinaceous inhibitor UGI

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4		17% PEG 4000, 4% PEG 550 MME, 0.27M LITHIUM SULFATE, 0.01M SODIUM BROMIDE, 0.1M TRIS-HCL, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.21	α = 90
b = 86.92	β = 90.35
c = 175.37	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	ADSC QUANTUM 210		2009-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.94	175	91.2	0.073	10.76	2.94		199006			29.86

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	2.04	86.6		0.413	3.29	3.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.93	29.48	199005	10083	89.8	0.2393	0.2369	0.2834	RANDOM	25.036

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]
13.15		-4.31	5.65		-18.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.884
r_dihedral_angle_4_deg	15.505
r_dihedral_angle_3_deg	14.69
r_dihedral_angle_1_deg	6.427
r_mcangle_it	2.997
r_mcbond_it	2.193
r_mcbond_other	2.192
r_angle_refined_deg	1.668
r_angle_other_deg	0.866
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.884
r_dihedral_angle_4_deg	15.505
r_dihedral_angle_3_deg	14.69
r_dihedral_angle_1_deg	6.427
r_mcangle_it	2.997
r_mcbond_it	2.193
r_mcbond_other	2.192
r_angle_refined_deg	1.668
r_angle_other_deg	0.866
r_chiral_restr	0.103
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19472
Nucleic Acid Atoms
Solvent Atoms	1483
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.