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Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with phosphate and acetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SmPNP refined at 1.9 angstrons
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 PEG 1500, Glycerol, Acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.962 α = 90 b = 120.202 β = 90 c = 131.957 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 IMAGE PLATE MARRESEARCH mirrors 2003-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 25.82 95.5 0.085 0.071 4.8 50988 2 2
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 2 2.11 89.7 0.495 0.39 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Rigid Body THROUGHOUT SmPNP refined at 1.9 angstrons 2 25.82 2 50931 48343 2588 95.14 0.188 0.18799 0.18664 0.21329 0.2049 RANDOM 23.515
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 Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.344 r_scangle_it 1.669 r_angle_refined_deg 1.02 r_scbond_it 0.942 r_mcangle_it 0.836 r_angle_other_deg 0.735 r_mcbond_it 0.449 r_nbd_other 0.215 r_symmetry_vdw_other 0.205 r_nbd_refined 0.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.344 r_scangle_it 1.669 r_angle_refined_deg 1.02 r_scbond_it 0.942 r_mcangle_it 0.836 r_angle_other_deg 0.735 r_mcbond_it 0.449 r_nbd_other 0.215 r_symmetry_vdw_other 0.205 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.152 r_symmetry_vdw_refined 0.127 r_xyhbond_nbd_refined 0.104 r_nbtor_other 0.077 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 6341 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling