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Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with acetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SmPNP refined at 2.1 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 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.231 α = 90 b = 120.212 β = 90 c = 131.933 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 Si 111 2002-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.98 SRS PX14.2
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 1.9 54 93.5 0.07 0.063 2.5 61501 58392 2.3 2.3
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) Redundancy Number Unique Reflections (All) 1 1.9 2 89.3 0.4 0.31 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SmPNP refined at 2.1 angstrons 1.9 45 2.3 2.3 61501 58392 3109 93.5 0.18875 0.1875 0.1871 0.21011 0.2179 RANDOM 22.692
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 Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.365 r_scangle_it 2.007 r_scbond_it 1.142 r_angle_refined_deg 1.051 r_mcangle_it 0.935 r_angle_other_deg 0.738 r_mcbond_it 0.501 r_nbd_other 0.217 r_symmetry_vdw_other 0.196 r_nbd_refined 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.365 r_scangle_it 2.007 r_scbond_it 1.142 r_angle_refined_deg 1.051 r_mcangle_it 0.935 r_angle_other_deg 0.738 r_mcbond_it 0.501 r_nbd_other 0.217 r_symmetry_vdw_other 0.196 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.114 r_nbtor_other 0.078 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6342 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing