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Crystal structure of USP7 in complex with the covalent inhibitor, FT827
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 7.5 293 20 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 7.5, 0.2 M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.5 50.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.81 α = 105.05 b = 63.31 β = 107.88 c = 65.66 γ = 113.03
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 PILATUS 6M-F 2014-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979490 Diamond I04
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 2.33 52.5 97 0.041 10.9 2.7 33087
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 2.33 2.39 96.4 0.588 0.811 2.8 2428
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 2.33 50 31606 1471 96.99 0.19081 0.18802 0.1922 0.2469 0.2512 RANDOM 73.06
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] -0.04 -0.1 -0.09 -0.15 -0.04 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.395 r_dihedral_angle_4_deg 21.04 r_dihedral_angle_3_deg 15.941 r_long_range_B_refined 7.63 r_long_range_B_other 7.629 r_dihedral_angle_1_deg 6.65 r_scangle_other 6.305 r_mcangle_it 5.216 r_mcangle_other 5.215 r_scbond_it 4.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.395 r_dihedral_angle_4_deg 21.04 r_dihedral_angle_3_deg 15.941 r_long_range_B_refined 7.63 r_long_range_B_other 7.629 r_dihedral_angle_1_deg 6.65 r_scangle_other 6.305 r_mcangle_it 5.216 r_mcangle_other 5.215 r_scbond_it 4.484 r_scbond_other 4.48 r_mcbond_other 3.837 r_mcbond_it 3.836 r_angle_refined_deg 1.566 r_angle_other_deg 1.018 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 5083 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing