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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 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.615 α = 90 b = 67.83 β = 91.256 c = 78.636 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 Bruker PHOTON II 2014-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER X8 PROTEUM 1.542
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 2.7 21.65 99.4 0.1519 10.07 9.48 21676
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 2.7 2.8 0.6989 1.89
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 2.7 21.647 21665 1106 99.431 0.272 0.2686 0.2693 0.3304 0.3301 50.379
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] 0.374 1.479 -0.73 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.92 r_dihedral_angle_6_deg 14.094 r_dihedral_angle_2_deg 12.573 r_lrange_other 9.859 r_lrange_it 9.857 r_dihedral_angle_1_deg 7.598 r_mcangle_other 5.327 r_mcangle_it 5.325 r_scangle_it 5.289 r_scangle_other 5.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.92 r_dihedral_angle_6_deg 14.094 r_dihedral_angle_2_deg 12.573 r_lrange_other 9.859 r_lrange_it 9.857 r_dihedral_angle_1_deg 7.598 r_mcangle_other 5.327 r_mcangle_it 5.325 r_scangle_it 5.289 r_scangle_other 5.289 r_mcbond_it 3.239 r_mcbond_other 3.239 r_scbond_it 3.129 r_scbond_other 3.128 r_angle_refined_deg 1.712 r_angle_other_deg 0.583 r_symmetry_xyhbond_nbd_refined 0.27 r_nbd_refined 0.241 r_symmetry_nbd_other 0.213 r_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.193 r_nbd_other 0.188 r_symmetry_xyhbond_nbd_other 0.181 r_ncsr_local_group_1 0.147 r_symmetry_nbd_refined 0.121 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5210 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling AMoRE phasing