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The Crystal Structure of SHP2 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1% Tryptone, 0.001M NaN3, 0.05M HEPEs-Na pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.617 α = 90 b = 213.636 β = 96.846 c = 55.707 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 PILATUS 6M 2022-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 49.12 98.8 0.111 4.2 2.8 32048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 0.319
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 2.6 49.12 32009 1564 98.735 0.241 0.2367 0.2399 0.3171 0.3191 34.279
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] 4.017 0.065 -2.343 -1.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.378 r_dihedral_angle_4_deg 19.894 r_dihedral_angle_3_deg 16.043 r_lrange_it 7.513 r_lrange_other 7.495 r_dihedral_angle_1_deg 6.661 r_mcangle_it 3.555 r_mcangle_other 3.555 r_scangle_it 3.08 r_scangle_other 3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.378 r_dihedral_angle_4_deg 19.894 r_dihedral_angle_3_deg 16.043 r_lrange_it 7.513 r_lrange_other 7.495 r_dihedral_angle_1_deg 6.661 r_mcangle_it 3.555 r_mcangle_other 3.555 r_scangle_it 3.08 r_scangle_other 3.08 r_mcbond_it 2.122 r_mcbond_other 2.122 r_scbond_it 1.823 r_scbond_other 1.823 r_angle_refined_deg 1.341 r_angle_other_deg 1.17 r_symmetry_xyhbond_nbd_refined 0.371 r_symmetry_nbd_refined 0.195 r_xyhbond_nbd_refined 0.194 r_nbd_other 0.189 r_symmetry_nbd_other 0.183 r_nbd_refined 0.175 r_nbtor_refined 0.158 r_xyhbond_nbd_other 0.143 r_ncsr_local_group_1 0.1 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7920 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing