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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 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.26 α = 90 b = 69.91 β = 132.308 c = 75.55 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 2012-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 2.46 29.2 93.9 0.043 8.99 1.81 99294
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 2.46 2.61 90.6 1.106 0.83
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 2.6 29.194 24986 1268 98.297 0.229 0.2237 0.2237 0.3206 0.3211 89.718
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] -0.371 0.224 1.844 -0.708
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 22.441 r_lrange_it 22.44 r_dihedral_angle_3_deg 20.975 r_scangle_it 19.787 r_scangle_other 19.785 r_mcangle_other 18.117 r_mcangle_it 18.116 r_scbond_it 16.233 r_scbond_other 16.23 r_dihedral_angle_2_deg 16.225
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 22.441 r_lrange_it 22.44 r_dihedral_angle_3_deg 20.975 r_scangle_it 19.787 r_scangle_other 19.785 r_mcangle_other 18.117 r_mcangle_it 18.116 r_scbond_it 16.233 r_scbond_other 16.23 r_dihedral_angle_2_deg 16.225 r_mcbond_it 14.978 r_mcbond_other 14.978 r_dihedral_angle_6_deg 14.127 r_dihedral_angle_1_deg 8.083 r_angle_refined_deg 2.522 r_angle_other_deg 0.814 r_symmetry_xyhbond_nbd_refined 0.692 r_nbd_other 0.245 r_nbd_refined 0.234 r_symmetry_nbd_other 0.218 r_nbtor_refined 0.195 r_symmetry_nbd_refined 0.184 r_xyhbond_nbd_refined 0.181 r_ncsr_local_group_1 0.129 r_chiral_restr 0.121 r_symmetry_xyhbond_nbd_other 0.109 r_symmetry_nbtor_other 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5387 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing