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Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with Non-detergent Sulfobetaine 195 and acetate
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 0.1952 0.20127 0.2154 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
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