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Crystal structure of the apo-form of USP7 catalytic domain [V302K] mutant
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, HANGING DROP 7 292 1% Tryptone, 0.05M HEPES Na pH 7.0, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.62 α = 90 b = 68.28 β = 95.99 c = 77.06 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 CCD ADSC QUANTUM 315r 2016-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.98 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.2 56.72 99.6 0.054 0.065 0.035 0.999 10 3.3 39712 41.67
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 2.2 2.27 99.3 0.541 0.805 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1NB8 2.2 56.719 1.33 39552 2000 99.22 0.216 0.2128 0.2234 0.2763 0.2827 54.4187
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.757 f_angle_d 1.198 f_chiral_restr 0.064 f_bond_d 0.014 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5381 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 12
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction