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human purine nucleoside phosphorylase in complex with JS-196
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.3 M magnesium chloride, 0.3 M calcium chloride, 20% w/v PEG 8000, 40% v/v ethylene glycol, 0.1 M MES/Imidazol, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.6 52.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.12 α = 90 b = 185.1 β = 119.94 c = 79.18 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 2019-10-18 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 1.8 50 85.8 0.97 13.26 3.56 156419
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 1.8 1.85 0.442
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 3PHB 1.8 38.76 154865 1565 86.06 0.2255 0.2251 0.2309 0.2675 0.2747 RANDOM 27.5
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.335 r_dihedral_angle_4_deg 19.194 r_dihedral_angle_3_deg 13.262 r_dihedral_angle_1_deg 6.711 r_angle_other_deg 2.312 r_angle_refined_deg 1.682 r_chiral_restr 0.079 r_bond_other_d 0.035 r_gen_planes_other 0.012 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.335 r_dihedral_angle_4_deg 19.194 r_dihedral_angle_3_deg 13.262 r_dihedral_angle_1_deg 6.711 r_angle_other_deg 2.312 r_angle_refined_deg 1.682 r_chiral_restr 0.079 r_bond_other_d 0.035 r_gen_planes_other 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12684 Nucleic Acid Atoms Solvent Atoms 955 Heterogen Atoms 225
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing