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human purine nucleoside phosphorylase in complex with JS-379
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZSL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 15.00 % w/v Polyethylene glycol 8,000; 500 mM Lithium sulfate; 100 mM Sodium acetate; pH 4.6; 1 mM TEW
Crystal Properties Matthews coefficient Solvent content 74.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.72 α = 90 b = 141.72 β = 90 c = 162.44 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 PIXEL DECTRIS PILATUS 6M 2021-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
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 2.36 49.01 99.9 0.999 7.89 10.18 50135
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 2.36 2.5 0.351
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 7ZSL 2.36 49.01 24922 1090 99.9 0.222 0.2204 0.2267 0.2587 0.2571 RANDOM 66.426
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] -0.17 -0.09 -0.17 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.045 r_dihedral_angle_4_deg 20.02 r_dihedral_angle_3_deg 15.563 r_dihedral_angle_1_deg 7.234 r_angle_refined_deg 1.597 r_angle_other_deg 1.229 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.045 r_dihedral_angle_4_deg 20.02 r_dihedral_angle_3_deg 15.563 r_dihedral_angle_1_deg 7.234 r_angle_refined_deg 1.597 r_angle_other_deg 1.229 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2138 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 122
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing