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Crystal structure of SHP2 in complex with I-0436650
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M ammonium-acetate
18% (w/v) PEG 3350
0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.517 α = 90 b = 213.686 β = 96.496 c = 55.896 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 EIGER2 X CdTe 16M 2022-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.196 44.243 95.9 0.0998 0.1167 0.0595 0.995 9.83 3.82 51600
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.196 2.234 98 0.6288 0.7482 0.3971 0.71 2.17 3.36 2644
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 2.197 44.243 51573 1351 95.829 0.232 0.2302 0.234 0.2877 0.2845 37.818
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] 2.228 0.428 -1.05 -1.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.599 r_dihedral_angle_other_3_deg 25.261 r_dihedral_angle_4_deg 16.581 r_dihedral_angle_6_deg 14.844 r_dihedral_angle_3_deg 13.651 r_dihedral_angle_1_deg 6.633 r_lrange_it 4.758 r_lrange_other 4.732 r_mcangle_it 3.095 r_mcangle_other 3.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.599 r_dihedral_angle_other_3_deg 25.261 r_dihedral_angle_4_deg 16.581 r_dihedral_angle_6_deg 14.844 r_dihedral_angle_3_deg 13.651 r_dihedral_angle_1_deg 6.633 r_lrange_it 4.758 r_lrange_other 4.732 r_mcangle_it 3.095 r_mcangle_other 3.094 r_scangle_it 2.629 r_scangle_other 2.629 r_mcbond_it 1.818 r_mcbond_other 1.818 r_scbond_it 1.55 r_scbond_other 1.547 r_angle_refined_deg 1.319 r_angle_other_deg 1.124 r_symmetry_xyhbond_nbd_refined 0.158 r_nbd_other 0.155 r_symmetry_nbd_other 0.152 r_nbd_refined 0.151 r_nbtor_refined 0.145 r_symmetry_nbd_refined 0.141 r_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.067 r_chiral_restr 0.05 r_ncsr_local_group_1 0.037 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8047 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 78
Software Software Software Name Purpose autoPROC data processing Aimless data scaling TRUNCATE data processing REFMAC refinement PHASER phasing