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Crystal structure of the tyrosine phosphatase SHP-2 with D61G 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 7.9 293 0.02M DDT, 0.1M Tris pH7.9, 13% PEG4000, 0.1M LiCl , VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.979 α = 90 b = 220.277 β = 90 c = 41.648 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 2011-11-09 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 2.2 40 99.3 0.1056 11.1 6.25 26872 26689 2 2 38.28
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 2.2 2.3 96.2 0.5204 2.68 6.09 3406
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 2.2 38.96 26872 26572 1339 99.72 0.2108 0.2108 0.2096 0.2217 0.2327 0.2421 RANDOM 44.5
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] 3.0771 3.5759 -6.653
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.13 t_omega_torsion 2.29 t_angle_deg 0.99 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 20.13 t_omega_torsion 2.29 t_angle_deg 0.99 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 4021 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 20
Software Software Software Name Purpose JBluIce-EPICS data collection PHASER phasing BUSTER refinement XDS data reduction XSCALL data scaling