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Crystal structure of a highly specific and potent USP7 ubiquitin variant inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 1.2 M sodium citrate, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.02 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.011 α = 90 b = 30.83 β = 97.26 c = 51.046 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 X 6M 2016-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97891 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 50 98.8 0.085 0.094 0.04 5.9 5.3 22616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 97.4 0.535 0.602 0.268 0.792 4.5
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 4AP4 1.51 50.01 21344 1263 98.72 0.1616 0.1598 0.171 0.1899 0.2013 RANDOM 18.028
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] -0.48 -0.44 1.33 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.895 r_dihedral_angle_4_deg 18.986 r_dihedral_angle_3_deg 11.109 r_dihedral_angle_1_deg 6.187 r_angle_refined_deg 1.442 r_angle_other_deg 0.948 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.895 r_dihedral_angle_4_deg 18.986 r_dihedral_angle_3_deg 11.109 r_dihedral_angle_1_deg 6.187 r_angle_refined_deg 1.442 r_angle_other_deg 0.948 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1227 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing DENZO data reduction