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SOS2 crystal structure with fragment bound (compound 13)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Used apo as initial model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281.15 10% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.396 α = 84.97 b = 52.008 β = 75.59 c = 60.918 γ = 76.07
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 S 6M 2022-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.1808 CLSI 08B1-1
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 2.12 43.8 95.5 0.99 8.52 3 29014
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 2.12 2.18 0.28 0.72
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 2.12 43.8 27579 1436 95.49 0.21527 0.21231 0.2162 0.27192 0.2752 RANDOM 46.848
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] 0.45 -0.31 -0.5 0.36 -1.22 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_3_deg 18.903 r_dihedral_angle_4_deg 17.181 r_long_range_B_refined 8.724 r_long_range_B_other 8.723 r_dihedral_angle_1_deg 7.066 r_scangle_other 6.746 r_mcangle_other 5.939 r_mcangle_it 5.937 r_scbond_it 4.699
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_3_deg 18.903 r_dihedral_angle_4_deg 17.181 r_long_range_B_refined 8.724 r_long_range_B_other 8.723 r_dihedral_angle_1_deg 7.066 r_scangle_other 6.746 r_mcangle_other 5.939 r_mcangle_it 5.937 r_scbond_it 4.699 r_scbond_other 4.698 r_mcbond_it 4.155 r_mcbond_other 4.153 r_angle_refined_deg 1.576 r_angle_other_deg 1.285 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3815 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement autoPROC data processing XSCALE data scaling Coot model building