1EUG | pdb_00001eug

CRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE AND ITS COMPLEXES WITH URACIL AND GLYCEROL: STRUCTURE AND GLYCOSYLASE MECHANISM REVISITED

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		PROTEIN CONCENTRATION 14.9 MG/ML, 0.2 M SODIUM ACETATE, 30% PEG4000, 0.1 M TRIS BUFFER, PH 8.5 USING HANGING DROP AT 293K.

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.13	α = 90
b = 61.32	β = 90
c = 64.4	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	AREA DETECTOR	BRUKER		1997-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER

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	1.6	99	97.9	0.095	7.3	4.2		27664		1.5

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	1.6	1.7	97.9		0.28	3.1	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	PDB ENTRY 1UDG	1.6	99	1	24809	1305	92.5	0.194	0.202		0.33	0.25	EVERY 20TH REFLECTION

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		2117

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.06
s_non_zero_chiral_vol	0.05
s_zero_chiral_vol	0.041
s_from_restr_planes	0.026
s_angle_d	0.024
s_anti_bump_dis_restr	0.012
s_bond_d	0.008
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1790
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms

Software

Software
Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
AMoRE	phasing
SHELXL-97	refinement

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.