Experiment: 2D3Y

Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M MES, 11.5% PEG3350, 0.2M Ammonium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.944889	36.757332

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.18	α = 90
b = 62.35	β = 90
c = 63.04	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 V		2004-06-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210		2004-05-27	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	0.9797	SPring-8	BL45XU
2	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	0.97940,0.97280,0.9815,0.9791	SPring-8	BL44B2

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
1,2	1.55	500	97	0.085	33.2	4.7	27453	27453		-3	9.9

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)
1,2	1.55	1.61	98.1		0.297	10.2	4.7	2719

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.55	50	27421	26992	2696	95	0.186	0.21	0.2095	random	11.2

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]
-0.02			1.19		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23
c_improper_angle_d	2.73
c_scangle_it	2.58
c_scbond_it	1.7
c_mcangle_it	1.32
c_angle_deg	1.3
c_mcbond_it	0.85
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1715
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	36

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement
HKL-2000	data reduction