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Crystal structure of SOS1-Nanobody77
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BKD 1BKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 ammonium sulfate 1.5 M, Tris 0.1 M pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.07 59.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.533 α = 90 b = 102.933 β = 90 c = 108.494 γ = 90
Symmetry Space Group P 21 21 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 EIGER2 XE 16M 2017-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
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 1.897935059 29.59 99.8 0.99 14.38 6.9 137616 37.2334274158
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 1.897935059 2.01 0.74
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BKD 1.89793505929 29.5898955693 1.34309844329 137508 6876 99.8257687952 0.182832527744 0.181392926296 0.1825 0.210625047888 0.2108 43.683619883
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.9756883879 f_angle_d 0.79606894041 f_chiral_restr 0.0507537985234 f_bond_d 0.0074973140948 f_plane_restr 0.00483796997781
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4612 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing