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SOS2 crystal structure with fragment bound (compound 14)
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% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.56 52.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.471 α = 85.05 b = 52.165 β = 75.37 c = 60.998 γ = 76.21
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 9M 2022-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.0332 CLSI 08ID-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 1.79 43.82 91.2 0.99 10.09 3.5 46269
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 1.79 1.84 0.32
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 1.79 43.82 44042 2225 91.28 0.19187 0.19003 0.1962 0.22792 0.2339 RANDOM 36.392
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] 0.87 -0.13 -0.15 -0.06 -1.39 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.164 r_dihedral_angle_3_deg 17.181 r_dihedral_angle_4_deg 15.821 r_long_range_B_refined 7.627 r_long_range_B_other 7.626 r_dihedral_angle_1_deg 6.167 r_scangle_other 5.842 r_mcangle_it 4.046 r_mcangle_other 4.045 r_scbond_it 3.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.164 r_dihedral_angle_3_deg 17.181 r_dihedral_angle_4_deg 15.821 r_long_range_B_refined 7.627 r_long_range_B_other 7.626 r_dihedral_angle_1_deg 6.167 r_scangle_other 5.842 r_mcangle_it 4.046 r_mcangle_other 4.045 r_scbond_it 3.797 r_scbond_other 3.796 r_mcbond_it 2.888 r_mcbond_other 2.86 r_angle_refined_deg 1.458 r_angle_other_deg 1.319 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 3847 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building