3H5Q

Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1M Tris, 0.2M ammonium sulfate, 25% PEG5K MME, 10mM Thymidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.591	α = 90
b = 40.885	β = 97.19
c = 105.578	γ = 90

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 315	MIRROR	2008-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9786	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	50	99	0.068	0.068	15.8	3.6		32421		-3	26.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.97	92.4		0.436	0.436	3.7	3

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	SAD	THROUGHOUT	1.94	43.87	32390	1632	98.87	0.168	0.166	0.204	RANDOM	20.09

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]
-0.5		-1.44	1.93		-1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.138
r_dihedral_angle_4_deg	15.351
r_dihedral_angle_3_deg	13.234
r_dihedral_angle_1_deg	5.487
r_scangle_it	5.135
r_scbond_it	3.136
r_mcangle_it	1.714
r_angle_refined_deg	1.696
r_angle_other_deg	1.003
r_mcbond_it	0.958
r_mcbond_other	0.289
r_chiral_restr	0.1
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3263
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	27

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing