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Mapping the SHP2 allosteric pocket with target-biased covalent fragments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (w/v) PEG 3350, 0.2M NaF, 0.1M Bis-Tris Propane pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.93 α = 90 b = 212.54 β = 95.23 c = 55.49 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 6M 2025-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 1.0332 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.35 49.027 94.9 0.023 0.995 7.7 7.5 40753
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.49 0.246 0.427
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.35 49.027 40751 2038 94.92 0.243 0.2405 0.2513 0.2831 0.2887 55.472
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] 6.32 -0.878 -4.244 -1.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.604 r_dihedral_angle_4_deg 19.533 r_dihedral_angle_3_deg 16.971 r_lrange_it 8.596 r_lrange_other 8.596 r_dihedral_angle_1_deg 6.838 r_mcangle_it 5.803 r_mcangle_other 5.803 r_scangle_it 5.327 r_scangle_other 5.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.604 r_dihedral_angle_4_deg 19.533 r_dihedral_angle_3_deg 16.971 r_lrange_it 8.596 r_lrange_other 8.596 r_dihedral_angle_1_deg 6.838 r_mcangle_it 5.803 r_mcangle_other 5.803 r_scangle_it 5.327 r_scangle_other 5.326 r_mcbond_it 3.497 r_mcbond_other 3.497 r_scbond_it 3.122 r_scbond_other 3.122 r_angle_refined_deg 1.288 r_angle_other_deg 1.111 r_nbd_refined 0.192 r_symmetry_nbd_other 0.176 r_nbd_other 0.162 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.139 r_symmetry_nbtor_other 0.07 r_ncsr_local_group_1 0.068 r_chiral_restr 0.048 r_symmetry_xyhbond_nbd_refined 0.01 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8004 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing