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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 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.05 α = 90 b = 68.28 β = 92 c = 77.66 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 2012-10-10 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 3.06 77.61 96.9 0.108 7.6 2.8 14565
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 3.06 3.14 98.8 0.619 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 3.06 77.61 14514 731 96.586 0.174 0.1694 0.1693 0.2639 0.2679 91.285
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] -4.248 -3.557 -1.747 6.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.295 r_lrange_it 18.052 r_lrange_other 18.052 r_dihedral_angle_6_deg 14.112 r_scangle_it 13.054 r_scangle_other 13.053 r_mcangle_it 11.229 r_mcangle_other 11.227 r_dihedral_angle_2_deg 9.272 r_scbond_it 8.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.295 r_lrange_it 18.052 r_lrange_other 18.052 r_dihedral_angle_6_deg 14.112 r_scangle_it 13.054 r_scangle_other 13.053 r_mcangle_it 11.229 r_mcangle_other 11.227 r_dihedral_angle_2_deg 9.272 r_scbond_it 8.369 r_scbond_other 8.368 r_mcbond_it 7.483 r_mcbond_other 7.467 r_dihedral_angle_1_deg 7.279 r_angle_refined_deg 1.525 r_angle_other_deg 0.53 r_symmetry_xyhbond_nbd_refined 0.379 r_xyhbond_nbd_other 0.237 r_nbd_refined 0.223 r_ncsr_local_group_1 0.223 r_symmetry_nbd_other 0.215 r_symmetry_nbd_refined 0.197 r_nbd_other 0.194 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.164 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5410 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing