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Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase: The M183L mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 200 mM Sodium Acetate, 20 %(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.5 α = 90 b = 132.5 β = 90 c = 115.82 γ = 90
Symmetry Space Group I 41 2 2
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-225 2017-07-12 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 2.6 93.69 99.9 0.99 18 16 16166
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 2.6 2.72 100 0.58 2 14.4
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 3PHC 2.6 93.69 15361 791 99.91 0.24409 0.24183 0.2418 0.28723 0.2882 RANDOM 79.173
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] -0.71 -0.71 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.485 r_dihedral_angle_3_deg 17.944 r_dihedral_angle_4_deg 14.455 r_long_range_B_other 11.535 r_long_range_B_refined 11.534 r_mcangle_it 8.289 r_mcangle_other 8.289 r_scangle_other 8.123 r_dihedral_angle_1_deg 6.924 r_mcbond_other 5.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.485 r_dihedral_angle_3_deg 17.944 r_dihedral_angle_4_deg 14.455 r_long_range_B_other 11.535 r_long_range_B_refined 11.534 r_mcangle_it 8.289 r_mcangle_other 8.289 r_scangle_other 8.123 r_dihedral_angle_1_deg 6.924 r_mcbond_other 5.374 r_mcbond_it 5.373 r_scbond_it 5.191 r_scbond_other 5.116 r_angle_refined_deg 1.486 r_angle_other_deg 0.968 r_chiral_restr 0.082 r_bond_refined_d 0.01 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 3315 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing