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Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671
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 8 293 25% (w/v) polyethylene glycol (PEG) 1500, 100 mM MMT pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.28 α = 90 b = 70.3 β = 97.17 c = 78.56 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 S 6M 2016-07-06 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 2.35 77.95 96.6 0.052 14.9 3.3 31221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 97.3 0.719 0.588 3.4 1564
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1NB8 2.35 50 29654 1551 96.6 0.21734 0.21448 0.2177 0.27214 0.2699 RANDOM 59.541
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] 1.6 -0.19 1.21 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.225 r_dihedral_angle_4_deg 21.214 r_dihedral_angle_3_deg 16.853 r_dihedral_angle_1_deg 6.192 r_long_range_B_refined 6.042 r_long_range_B_other 6.042 r_scangle_other 4.371 r_mcangle_it 3.6 r_mcangle_other 3.6 r_scbond_it 2.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.225 r_dihedral_angle_4_deg 21.214 r_dihedral_angle_3_deg 16.853 r_dihedral_angle_1_deg 6.192 r_long_range_B_refined 6.042 r_long_range_B_other 6.042 r_scangle_other 4.371 r_mcangle_it 3.6 r_mcangle_other 3.6 r_scbond_it 2.988 r_scbond_other 2.987 r_mcbond_it 2.482 r_mcbond_other 2.482 r_angle_refined_deg 1.574 r_angle_other_deg 1.056 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4990 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing