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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 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.764 α = 90 b = 67.688 β = 90.543 c = 77.513 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 2014-08-11 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 2.2 21.66 95.4 0.1689 5.91 3.81 37692
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 2.2 2.3 91 0.5394 1.55 2.17
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 21.66 20723 1042 96.719 0.276 0.273 0.273 0.3281 0.328 30.517
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] -15.773 -16.247 13.202 2.571
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.83 r_dihedral_angle_6_deg 16.265 r_dihedral_angle_2_deg 10.983 r_lrange_it 9.18 r_lrange_other 9.179 r_dihedral_angle_1_deg 7.287 r_mcangle_it 5.069 r_mcangle_other 5.069 r_scangle_it 5.026 r_scangle_other 5.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.83 r_dihedral_angle_6_deg 16.265 r_dihedral_angle_2_deg 10.983 r_lrange_it 9.18 r_lrange_other 9.179 r_dihedral_angle_1_deg 7.287 r_mcangle_it 5.069 r_mcangle_other 5.069 r_scangle_it 5.026 r_scangle_other 5.026 r_mcbond_it 3.094 r_mcbond_other 3.092 r_scbond_other 3.011 r_scbond_it 3.01 r_angle_refined_deg 1.88 r_angle_other_deg 0.636 r_symmetry_nbd_refined 0.485 r_nbd_other 0.406 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.236 r_symmetry_xyhbond_nbd_other 0.236 r_symmetry_nbd_other 0.219 r_ncsr_local_group_1 0.201 r_nbtor_refined 0.197 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.084 r_symmetry_xyhbond_nbd_refined 0.035 r_bond_refined_d 0.009 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 5273 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling AMoRE phasing