1TCU

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSmPNP refined at 1.9 angstrons

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5277PEG 1500, Glycerol, Acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.140.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.962α = 90
b = 120.202β = 90
c = 131.957γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHmirrors2003-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU ULTRAX 181.5418

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1225.8295.50.0850.0714.85098822
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)RedundancyNumber Unique Reflections (All)
122.1189.70.4950.391.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRigid BodyTHROUGHOUTSmPNP refined at 1.9 angstrons225.8225093148343258895.140.1880.187990.186640.21329RANDOM23.515
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.344
r_scangle_it1.669
r_angle_refined_deg1.02
r_scbond_it0.942
r_mcangle_it0.836
r_angle_other_deg0.735
r_mcbond_it0.449
r_nbd_other0.215
r_symmetry_vdw_other0.205
r_nbd_refined0.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.344
r_scangle_it1.669
r_angle_refined_deg1.02
r_scbond_it0.942
r_mcangle_it0.836
r_angle_other_deg0.735
r_mcbond_it0.449
r_nbd_other0.215
r_symmetry_vdw_other0.205
r_nbd_refined0.183
r_symmetry_hbond_refined0.152
r_symmetry_vdw_refined0.127
r_xyhbond_nbd_refined0.104
r_nbtor_other0.077
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6341
Nucleic Acid Atoms
Solvent Atoms608
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling