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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 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.94 α = 90 b = 66.78 β = 94.6 c = 76.31 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 2012-10-29 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 2.76 54.4 97 0.134 8.6 3 18158
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 2.76 2.83 99.2 0.737 2 3.2
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 2.76 54.4 18148 926 96.676 0.219 0.2138 0.214 0.3216 0.3205 61.915
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] 1.247 2.266 0.686 -2.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.941 r_lrange_it 18.929 r_lrange_other 18.928 r_dihedral_angle_6_deg 15.182 r_scangle_it 15.122 r_scangle_other 15.12 r_dihedral_angle_2_deg 15.058 r_mcangle_other 13.495 r_mcangle_it 13.492 r_scbond_it 10.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.941 r_lrange_it 18.929 r_lrange_other 18.928 r_dihedral_angle_6_deg 15.182 r_scangle_it 15.122 r_scangle_other 15.12 r_dihedral_angle_2_deg 15.058 r_mcangle_other 13.495 r_mcangle_it 13.492 r_scbond_it 10.668 r_scbond_other 10.667 r_mcbond_other 9.814 r_mcbond_it 9.813 r_dihedral_angle_1_deg 7.814 r_angle_refined_deg 2.23 r_angle_other_deg 0.739 r_nbd_refined 0.223 r_nbd_other 0.218 r_symmetry_nbd_other 0.213 r_ncsr_local_group_1 0.207 r_xyhbond_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.197 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.192 r_symmetry_xyhbond_nbd_other 0.149 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5253 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling AMoRE phasing