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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 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.84 α = 90 b = 70.58 β = 92.96 c = 78.59 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 2013-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.77 52.78 97.9 0.127 6.8 3.2 20568
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 2.77 2.84 98.6 0.768 1.5 3.3
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 2.77 52.78 20530 1050 97.646 0.188 0.1848 0.186 0.2433 0.2439 69.819
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 2.204 0.629 -1.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.654 r_lrange_other 15.68 r_lrange_it 15.679 r_dihedral_angle_6_deg 14.718 r_dihedral_angle_2_deg 14.395 r_scangle_it 10.903 r_scangle_other 10.901 r_mcangle_it 9.067 r_mcangle_other 9.065 r_scbond_it 6.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.654 r_lrange_other 15.68 r_lrange_it 15.679 r_dihedral_angle_6_deg 14.718 r_dihedral_angle_2_deg 14.395 r_scangle_it 10.903 r_scangle_other 10.901 r_mcangle_it 9.067 r_mcangle_other 9.065 r_scbond_it 6.975 r_scbond_other 6.974 r_dihedral_angle_1_deg 6.965 r_mcbond_it 6.079 r_mcbond_other 6.078 r_angle_refined_deg 1.689 r_angle_other_deg 0.58 r_nbd_refined 0.221 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.183 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_other 0.096 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.085 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 5415 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing