1TD1

Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with acetate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SmPNP refined at 2.1 angstrons

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277	PEG 1500, Glycerol, acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.231	α = 90
b = 120.212	β = 90
c = 131.933	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	CCD	ADSC QUANTUM 4	Si 111	2002-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.98	SRS	PX14.2

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	1.9	54	93.5	0.07	0.063		2.5	61501	58392	2.3	2.3

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	1.9	2	89.3		0.4	0.31	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	SmPNP refined at 2.1 angstrons	1.9	45	2.3	2.3	61501	58392	3109	93.5	0.18875	0.1875	0.1871	0.21011	RANDOM	22.692

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]
2.24			-0.73		-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.365
r_scangle_it	2.007
r_scbond_it	1.142
r_angle_refined_deg	1.051
r_mcangle_it	0.935
r_angle_other_deg	0.738
r_mcbond_it	0.501
r_nbd_other	0.217
r_symmetry_vdw_other	0.196
r_nbd_refined	0.186
r_symmetry_hbond_refined	0.157
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.114
r_nbtor_other	0.078
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6342
Nucleic Acid Atoms
Solvent Atoms	580
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing