1TCV

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)
TypeSourceAccession CodeDetails
experimental modelOtherThe starting model for molecular replacement was the SmPNP (purine nucleoside phosphorylase from S. mansoni) refined at 2.75 A resolution.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15277PEG 1500, Glycerol, acetete buffer, Non-detergent sulfobetaine 195, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00
Crystal Properties
Matthews coefficientSolvent content
2.140

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.755α = 90
b = 122.059β = 90
c = 129.761γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.7545.599.30.0940.0813.6784222.5
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)RedundancyNumber Unique Reflections (All)
1.751.8497.10.3520.2982.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTThe starting model for molecular replacement was the SmPNP (purine nucleoside phosphorylase from S. mansoni) refined at 2.75 A resolution.1.7587.717835474411394299.20.180.1790.20127RANDOM20.697
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]
0.290.65-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.362
r_angle_refined_deg1.154
r_angle_other_deg0.744
r_symmetry_vdw_other0.276
r_nbd_other0.23
r_nbd_refined0.199
r_symmetry_hbond_refined0.179
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.122
r_nbtor_other0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.362
r_angle_refined_deg1.154
r_angle_other_deg0.744
r_symmetry_vdw_other0.276
r_nbd_other0.23
r_nbd_refined0.199
r_symmetry_hbond_refined0.179
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.122
r_nbtor_other0.079
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms6269
Nucleic Acid Atoms
Solvent Atoms725
Heterogen Atoms48

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling