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Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 0.1 M HEPES pH 7.5, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.39 α = 90 b = 78.38 β = 108.63 c = 73.41 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 PILATUS 6M 2020-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.34 45.21 63.1 0.918 9.2 3.3 15966
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.42 0.848
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 (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 2.34 45.2 15966 817 63.12 0.21698 0.21277 0.22 0.29535 0.3 RANDOM 26.777
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] -0.05 0.05 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17 r_dihedral_angle_2_deg 13.931 r_dihedral_angle_1_deg 7.326 r_long_range_B_refined 5.416 r_long_range_B_other 5.4 r_mcangle_it 3.253 r_mcangle_other 3.252 r_scangle_other 2.654 r_mcbond_it 1.915 r_mcbond_other 1.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17 r_dihedral_angle_2_deg 13.931 r_dihedral_angle_1_deg 7.326 r_long_range_B_refined 5.416 r_long_range_B_other 5.4 r_mcangle_it 3.253 r_mcangle_other 3.252 r_scangle_other 2.654 r_mcbond_it 1.915 r_mcbond_other 1.915 r_scbond_it 1.59 r_scbond_other 1.59 r_angle_refined_deg 1.215 r_angle_other_deg 0.423 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4862 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing