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Crystal structure of Plasmodium falciparum purine nucleoside phosphorylase (V181D) mutant complexed with DADMe-ImmG and phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PHC PDB entry 3PHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 295 100 mM tri-sodium citrate, pH 5.6, 200 mM ammonium sulfate, 15% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.11 α = 90 b = 95.11 β = 90 c = 135.561 γ = 120
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 RAYONIX MX-225HE 2017-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.57 45.19 100 0.99 13.7 11.7 33133
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.6 100 0.75 1.9 8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3PHC 1.57 45.19 31499 1633 99.95 0.18486 0.18339 0.21474 0.2037 RANDOM 23.783
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] -1.42 -0.71 -1.42 4.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.64 r_dihedral_angle_4_deg 15.152 r_dihedral_angle_3_deg 11.604 r_dihedral_angle_1_deg 5.917 r_long_range_B_refined 4.479 r_long_range_B_other 4.478 r_scangle_other 2.705 r_mcangle_other 2.244 r_mcangle_it 2.242 r_scbond_it 1.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.64 r_dihedral_angle_4_deg 15.152 r_dihedral_angle_3_deg 11.604 r_dihedral_angle_1_deg 5.917 r_long_range_B_refined 4.479 r_long_range_B_other 4.478 r_scangle_other 2.705 r_mcangle_other 2.244 r_mcangle_it 2.242 r_scbond_it 1.616 r_scbond_other 1.615 r_angle_refined_deg 1.383 r_mcbond_it 1.313 r_mcbond_other 1.306 r_angle_other_deg 0.914 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other 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 1749 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing