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SHP2 in complex with a novel allosteric inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293.15 14.00 %w/v PEG 3350, 0.20 M NH4 Acetate, 0.10 M Tris pH=9.00
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.888 α = 90 b = 215.966 β = 95.11 c = 55.829 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 EIGER X 16M 2020-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.999987 NSLS X6A
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 2.236 107.983 90.3 0.996 8.4 4.4 34069
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 2.236 2.485 0.587
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 2.24 107.98 33212 857 67.01 0.21707 0.21589 0.2192 0.26379 0.2285 RANDOM 44.743
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] -2.31 -0.68 3.12 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.133 r_dihedral_angle_4_deg 17.393 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 6.389 r_long_range_B_refined 5.273 r_long_range_B_other 5.262 r_mcangle_it 3.054 r_mcangle_other 3.054 r_scangle_other 2.911 r_scbond_it 1.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.133 r_dihedral_angle_4_deg 17.393 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 6.389 r_long_range_B_refined 5.273 r_long_range_B_other 5.262 r_mcangle_it 3.054 r_mcangle_other 3.054 r_scangle_other 2.911 r_scbond_it 1.807 r_scbond_other 1.807 r_mcbond_it 1.788 r_mcbond_other 1.788 r_angle_refined_deg 1.518 r_angle_other_deg 1.228 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 7857 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing