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purine nucleoside phosphorylase in complex with JS-379
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.1 M Tris; 25 mM Magnesium chloride; 25% w/v PEG4000; pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.528 α = 90 b = 84.54 β = 94.47 c = 93.879 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2019-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
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 1.9 45.92 81.5 0.996 7.15 3.8 58542
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 1.9 1.95 0.44
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 1g2o 1.97 45.92 40903 2148 77.81 0.1921 0.189 0.1969 0.2526 0.2577 RANDOM 36.707
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] 0.04 0.02 -0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.03 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_3_deg 14.812 r_dihedral_angle_1_deg 7.479 r_angle_refined_deg 1.542 r_angle_other_deg 1.284 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.03 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_3_deg 14.812 r_dihedral_angle_1_deg 7.479 r_angle_refined_deg 1.542 r_angle_other_deg 1.284 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5678 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction XDS data scaling