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Crystal structure of the NTF2L domain of human G3BP1 in complex with small molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M MES pH 6.5, 15% PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.37 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.17 α = 90 b = 84.69 β = 91.26 c = 102.15 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 2M 2020-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9655 ESRF ID30B
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 2.68 46.87 96.51 0.875 0.281 1.05 23085
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.749 95.91 0.337
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 2.68 46.87 23085 1165 96.51 0.28101 0.27558 0.2776 0.39465 0.3947 RANDOM 34.201
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 0.05 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.139 r_dihedral_angle_2_deg 9.012 r_dihedral_angle_1_deg 8.242 r_long_range_B_refined 6.414 r_long_range_B_other 6.413 r_mcangle_it 3.609 r_mcangle_other 3.608 r_scangle_other 3.125 r_mcbond_it 2.179 r_mcbond_other 2.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.139 r_dihedral_angle_2_deg 9.012 r_dihedral_angle_1_deg 8.242 r_long_range_B_refined 6.414 r_long_range_B_other 6.413 r_mcangle_it 3.609 r_mcangle_other 3.608 r_scangle_other 3.125 r_mcbond_it 2.179 r_mcbond_other 2.178 r_scbond_it 1.915 r_scbond_other 1.915 r_angle_refined_deg 1.179 r_angle_other_deg 0.421 r_chiral_restr 0.052 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 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 6069 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 291
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction PHASER phasing