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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 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.754 α = 90 b = 70.461 β = 92.905 c = 77.946 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 2013-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0723 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.86 50 96.7 0.066 0.081 0.047 8.9 2.9 18505
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 2.96 99 0.574 0.705 0.404 1.7 2.9
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 2.86 43.726 18491 948 96.458 0.202 0.1974 0.1983 0.2778 0.2789 91.823
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] -5.192 -2.297 0.864 4.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.466 r_lrange_other 17.966 r_lrange_it 17.965 r_dihedral_angle_6_deg 14.749 r_scangle_it 12.448 r_scangle_other 12.447 r_mcangle_other 11.576 r_mcangle_it 11.575 r_dihedral_angle_2_deg 9.478 r_scbond_it 8.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.466 r_lrange_other 17.966 r_lrange_it 17.965 r_dihedral_angle_6_deg 14.749 r_scangle_it 12.448 r_scangle_other 12.447 r_mcangle_other 11.576 r_mcangle_it 11.575 r_dihedral_angle_2_deg 9.478 r_scbond_it 8.229 r_scbond_other 8.228 r_mcbond_it 7.878 r_mcbond_other 7.876 r_dihedral_angle_1_deg 7.429 r_angle_refined_deg 1.652 r_angle_other_deg 0.558 r_symmetry_xyhbond_nbd_refined 0.274 r_nbd_other 0.26 r_nbd_refined 0.235 r_symmetry_nbd_other 0.212 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.185 r_symmetry_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.122 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.08 r_bond_refined_d 0.006 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 5310 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling AMoRE phasing