1TD1

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSmPNP refined at 2.1 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
2.140.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.231α = 90
b = 120.212β = 90
c = 131.933γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Si 1112002-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.20.98SRSPX14.2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95493.50.070.0632.561501583922.32.3
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)RedundancyNumber Unique Reflections (All)
11.9289.30.40.312.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSmPNP refined at 2.1 angstrons1.9452.32.36150158392310993.50.188750.18750.18710.21011RANDOM22.692
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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.365
r_scangle_it2.007
r_scbond_it1.142
r_angle_refined_deg1.051
r_mcangle_it0.935
r_angle_other_deg0.738
r_mcbond_it0.501
r_nbd_other0.217
r_symmetry_vdw_other0.196
r_nbd_refined0.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.365
r_scangle_it2.007
r_scbond_it1.142
r_angle_refined_deg1.051
r_mcangle_it0.935
r_angle_other_deg0.738
r_mcbond_it0.501
r_nbd_other0.217
r_symmetry_vdw_other0.196
r_nbd_refined0.186
r_symmetry_hbond_refined0.157
r_symmetry_vdw_refined0.147
r_xyhbond_nbd_refined0.114
r_nbtor_other0.078
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6342
Nucleic Acid Atoms
Solvent Atoms580
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing