1TCV | pdb_00001tcv

Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with Non-detergent Sulfobetaine 195 and acetate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		The starting model for molecular replacement was the SmPNP (purine nucleoside phosphorylase from S. mansoni) refined at 2.75 A resolution.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5	277	PEG 1500, Glycerol, acetete buffer, Non-detergent sulfobetaine 195, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00

Crystal Properties
Matthews coefficient	Solvent content
2.1	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.755	α = 90
b = 122.059	β = 90
c = 129.761	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		2001-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.75	45.5	99.3	0.094	0.081		3.6		78422		2.5

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)
	1.75	1.84	97.1		0.352	0.298	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	The starting model for molecular replacement was the SmPNP (purine nucleoside phosphorylase from S. mansoni) refined at 2.75 A resolution.	1.75	87.71	78354	74411	3942	99.2	0.18	0.179	0.2	0.20127	0.22	RANDOM	20.697

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]
0.29			0.65		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.362
r_angle_refined_deg	1.154
r_angle_other_deg	0.744
r_symmetry_vdw_other	0.276
r_nbd_other	0.23
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.179
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.122
r_nbtor_other	0.079
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6269
Nucleic Acid Atoms
Solvent Atoms	725
Heterogen Atoms	48

Software

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