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Crystal Structure of Monobody Mb(SHP2PTP_13)/SHP2 PTP Domain Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZM1 PDB entries 3ZM1 & 3K2M experimental model PDB 3K2M PDB entries 3ZM1 & 3K2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 292 0.1 M sodium citrate tribasic dihydrate, 2% Tascimate, 16% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.46 α = 80.14 b = 48.49 β = 77.53 c = 102.07 γ = 61.63
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2015-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
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 2.39 49.67 93.3 0.084 0.118 0.084 0.974 6.7 1.8 29422 25.39
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) 1 2.39 2.48 92.1 0.245 0.347 0.245 0.531 2.3 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entries 3ZM1 & 3K2M 2.39 49.67 2.02 28944 1473 91.84 0.2306 0.2291 0.2291 0.2588 0.2593 34.15
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 5.355 f_angle_d 0.5348 f_chiral_restr 0.0452 f_plane_restr 0.0033 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5491 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHASER phasing