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Crystal structure of the Plasmodium falciparum purine nucleoside phosphorylase complexed with inosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LX7 PDB ENTRY 1LX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 10 % PEG 8000, 0.1 M HEPES PH 7.5, 30 % HEXANETRIOL
Crystal Properties Matthews coefficient Solvent content 2.3 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.117 α = 90 b = 95.117 β = 90 c = 47.075 γ = 120
Symmetry Space Group P 3 2 1
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 CCD 2003-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 20 87 0.08 10 2.5 27984
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 80 0.35 5 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 1LX7 2 18.9 14648 788 91.6 0.268 0.264 0.2638 0.342 0.3434 RANDOM 38.57
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] 0.96 0.48 0.96 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.3 r_dihedral_angle_3_deg 19.971 r_dihedral_angle_4_deg 17.495 r_dihedral_angle_1_deg 8.281 r_scangle_it 3.808 r_scbond_it 3.004 r_angle_refined_deg 1.931 r_mcangle_it 1.678 r_mcbond_it 1.002 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.3 r_dihedral_angle_3_deg 19.971 r_dihedral_angle_4_deg 17.495 r_dihedral_angle_1_deg 8.281 r_scangle_it 3.808 r_scbond_it 3.004 r_angle_refined_deg 1.931 r_mcangle_it 1.678 r_mcbond_it 1.002 r_nbtor_refined 0.321 r_nbd_refined 0.292 r_symmetry_vdw_refined 0.282 r_xyhbond_nbd_refined 0.271 r_symmetry_hbond_refined 0.238 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1847 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing