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Structure-guided discovery of selective USP7 inhibitors with in vivo activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 23% peg 3350,
0.6 M sodium formate,
10 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.88 α = 90 b = 68.23 β = 92.22 c = 76.88 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 PILATUS3 6M 2014-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.37 52.59 96.5 0.075 12.7 2.8 10728
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 3.37 3.46 0.806 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.37 52.59 10727 556 96.362 0.193 0.1876 0.1873 0.2969 0.299 121.291
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] -0.044 -0.982 -6.682 6.781
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.102 r_lrange_other 23.102 r_dihedral_angle_3_deg 18.819 r_mcangle_it 16.626 r_mcangle_other 16.625 r_scangle_it 16.26 r_scangle_other 16.258 r_dihedral_angle_6_deg 13.653 r_mcbond_it 10.913 r_mcbond_other 10.913
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.102 r_lrange_other 23.102 r_dihedral_angle_3_deg 18.819 r_mcangle_it 16.626 r_mcangle_other 16.625 r_scangle_it 16.26 r_scangle_other 16.258 r_dihedral_angle_6_deg 13.653 r_mcbond_it 10.913 r_mcbond_other 10.913 r_scbond_it 10.525 r_scbond_other 10.524 r_dihedral_angle_1_deg 7.65 r_dihedral_angle_2_deg 5.03 r_angle_refined_deg 1.454 r_angle_other_deg 0.511 r_symmetry_nbd_refined 0.352 r_nbd_other 0.237 r_nbd_refined 0.234 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.187 r_ncsr_local_group_1 0.171 r_xyhbond_nbd_refined 0.165 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.059 r_symmetry_xyhbond_nbd_refined 0.037 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_chiral_restr_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5326 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing