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Crystal structure of the tyrosine phosphatase SHP-2 with Q506P mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SHP PDB ENTRY 2SHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 0.02M DDT, 0.1M Tris pH8.0, 19% PEG4000, 10% Glycerol, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.91 35.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.79 α = 90 b = 202.35 β = 90 c = 44.46 γ = 90
Symmetry Space Group P 21 21 2
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 2011-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
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 2.7 40 99.9 0.1386 12.05 6.45 14356 14342 2 2 53.56
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 2.7 2.8 100 0.5595 2.81 6.25 1449
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2SHP 2.7 37.12 14356 14298 1099 99.99 0.2272 0.2272 0.2259 0.2397 0.2419 0.254 RANDOM 42.97
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] -4.3378 9.1521 -4.8142
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.37 t_omega_torsion 1.85 t_angle_deg 0.91 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.37 t_omega_torsion 1.85 t_angle_deg 0.91 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3951 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 36
Software Software Software Name Purpose JBluIce-EPICS data collection PHASER phasing BUSTER refinement XDS data reduction XSCALL data scaling