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Crystal structure of the NTF2L domain of human G3BP1 in complex with the USP10 derived peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FCJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.1 M Sodium citrate tribasic dihydrate pH 5.0; 19 % w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.874 α = 90 b = 81.874 β = 90 c = 94.247 γ = 120
Symmetry Space Group P 31 2 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 EIGER X 16M 2019-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97915 SSRF BL17U1
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 2.68 70.9 92.7 0.093 0.099 0.034 57.1 8.8 9910
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 2.68 2.73 0.528 0.561 0.187 0.934 5.1
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 4fcj 2.68 70.9 9408 482 92.39 0.2127 0.2103 0.2234 0.2543 0.233 RANDOM 54.434
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] -0.74 -0.37 -0.74 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.049 r_dihedral_angle_4_deg 19.853 r_dihedral_angle_3_deg 19.546 r_dihedral_angle_1_deg 7.326 r_angle_refined_deg 1.728 r_angle_other_deg 1.028 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.049 r_dihedral_angle_4_deg 19.853 r_dihedral_angle_3_deg 19.546 r_dihedral_angle_1_deg 7.326 r_angle_refined_deg 1.728 r_angle_other_deg 1.028 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2258 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing