3CXM

Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	1.3 M Potassium phosphate dibasic, 0.1 M Sodium acetate pH 4.5, 5 mM DTT, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.32	α = 90
b = 75.32	β = 90
c = 105.703	γ = 120

Symmetry
Space Group	P 61

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	MARMOSAIC 325 mm CCD	Mirrors	2007-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91724	SSRL	BL9-2

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	1.5	50	97.2	0.045	14.3	10.2		52821			21.8

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	1.5	1.55	79.9		0.62	1.5	5.3	4325

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1EUI	1.5	37.66	52760	2693	97.21	0.139	0.138	0.16	RANDOM	15.353

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]
0.34	0.17		0.34		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.475
r_dihedral_angle_4_deg	20.401
r_dihedral_angle_3_deg	11.752
r_scangle_it	7.073
r_dihedral_angle_1_deg	5.926
r_scbond_it	4.406
r_mcangle_it	3.259
r_mcbond_it	2.033
r_angle_refined_deg	1.623
r_angle_other_deg	0.974
r_mcbond_other	0.682
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1933
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling