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Crystal structure of purine nucleoside phosphorylase (E258D, L261A) mutant from human 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 8.5 295 Protein (10 mg/mL); Reservoir (0.2 M lithium sulfate, 0.1 M TRIS-HCl, pH 8.5 and 20% (w/v) PEG 4000)
Crystal Properties Matthews coefficient Solvent content 2.91 57.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 268.808 α = 90 b = 58.845 β = 112.92 c = 173.155 γ = 90
Symmetry Space Group C 1 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 RAYONIX MX225HE 2015-11-04 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 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 2.3 50 99.2 0.095 16.3 7.47 112272 105996 46
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 2.3 2.43 96.4 0.777 2.82 7.51
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 2.3 25 105996 5579 99.8 0.1797 0.1781 0.1838 0.2109 0.2109 RANDOM 43.583
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] -1.45 -0.57 2.4 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.902 r_dihedral_angle_4_deg 17.245 r_dihedral_angle_3_deg 15.078 r_dihedral_angle_1_deg 6.477 r_mcangle_it 3.887 r_mcbond_it 2.518 r_mcbond_other 2.518 r_angle_refined_deg 1.527 r_angle_other_deg 0.96 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.902 r_dihedral_angle_4_deg 17.245 r_dihedral_angle_3_deg 15.078 r_dihedral_angle_1_deg 6.477 r_mcangle_it 3.887 r_mcbond_it 2.518 r_mcbond_other 2.518 r_angle_refined_deg 1.527 r_angle_other_deg 0.96 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13365 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 180
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction