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Structure-based Discovery of Novel non-Covalent Small Molecule Inhibitors of USP30
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.007 α = 90 b = 60.881 β = 90 c = 102.507 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 ADSC QUANTUM 315r 2022-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.58 47.08 99.5 0.22 0.243 0.103 0.99 6.1 5.4 10967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.69 96.4 1.41 1.554 0.642 0.464 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.58 47.08 1.34 10909 1092 99.45 0.2268 0.2216 0.2218 0.2724 0.2739
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 f_dihedral_angle_d 5.043 f_angle_d 0.727 f_chiral_restr 0.043 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2299 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing