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Structure of human SHOC2 in complex with a small molecule inhibitor (R)-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YTG SHOC2 apo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 See reference. Crystals of apo SHOC2 in space group p212121 were incubated with compound and harvested. 0.05 M Tris (7.0), 40% (v/v) Pentaerythritol Propoxylate 5/4 PO/OH, 0.2 M KCl
Crystal Properties Matthews coefficient Solvent content 2.32 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.839 α = 90 b = 70.137 β = 90 c = 199.041 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 EIGER X 9M 2022-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.676 66.15 100 0.223 0.995 9.4 9.7 15738 42.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.676 2.685 99.7 1.528 0.703 2 10.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.68 40.58 1.34 15729 770 99.97 0.1981 0.1941 0.1945 0.2752 0.2722 40.01
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 17.6392 f_angle_d 1.0428 f_chiral_restr 0.0501 f_bond_d 0.0085 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3916 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement PHASER phasing autoPROC data processing