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Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PHB PDB entry 3PHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 100 mM HEPES, pH 7.5, 0.2 M lithium sulfate, 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.08 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.96 α = 90 b = 124.27 β = 90 c = 136.73 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 RAYONIX MX225HE 2016-10-18 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) R Merge I (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 2.2 69.26 100 0.17 0.99 5.8 6.6 91303 24
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 2.2 2.24 100 0.71 1.8 6
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 3PHB 2.2 69.26 86719 4492 99.96 0.21503 0.21382 0.2194 0.23809 0.2421 RANDOM 34.993
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] 2.72 -1.13 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.537 r_dihedral_angle_3_deg 13.746 r_dihedral_angle_4_deg 12.032 r_long_range_B_refined 6.501 r_long_range_B_other 6.501 r_dihedral_angle_1_deg 6.178 r_mcangle_it 3.195 r_mcangle_other 3.195 r_scangle_other 2.526 r_mcbond_it 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.537 r_dihedral_angle_3_deg 13.746 r_dihedral_angle_4_deg 12.032 r_long_range_B_refined 6.501 r_long_range_B_other 6.501 r_dihedral_angle_1_deg 6.178 r_mcangle_it 3.195 r_mcangle_other 3.195 r_scangle_other 2.526 r_mcbond_it 1.78 r_mcbond_other 1.78 r_scbond_it 1.429 r_scbond_other 1.429 r_angle_refined_deg 1.368 r_angle_other_deg 0.931 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 13348 Nucleic Acid Atoms Solvent Atoms 713 Heterogen Atoms 265
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing