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Protein Tyrosine Phosphatase 1B, D289A mutant, apo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B90 PDB entry 6B90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 100 mM HEPES, 200 mM magnesium acetate, 14% PEG8000
Crystal Properties Matthews coefficient Solvent content 3.17 61.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.314 α = 90 b = 88.314 β = 90 c = 104.155 γ = 120
Symmetry Space Group P 31 2 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 PILATUS3 S 6M 2020-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 1.8 76.48 100 0.178 0.187 0.056 0.997 6.2 10.8 40989 23.27
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 1.8 1.83 100 0.315 0.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 6B90 1.8 76.48 40989 2139 98.03 0.20561 0.20351 0.24369 0.2204 RANDOM 38.766
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] 0.23 0.12 0.23 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.349 r_dihedral_angle_4_deg 15.843 r_dihedral_angle_3_deg 15.198 r_long_range_B_other 11.235 r_long_range_B_refined 11.207 r_scangle_other 9.034 r_mcangle_it 7.273 r_mcangle_other 7.272 r_scbond_it 6.579 r_scbond_other 6.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.349 r_dihedral_angle_4_deg 15.843 r_dihedral_angle_3_deg 15.198 r_long_range_B_other 11.235 r_long_range_B_refined 11.207 r_scangle_other 9.034 r_mcangle_it 7.273 r_mcangle_other 7.272 r_scbond_it 6.579 r_scbond_other 6.576 r_dihedral_angle_1_deg 6.31 r_mcbond_it 5.401 r_mcbond_other 5.38 r_angle_refined_deg 1.418 r_angle_other_deg 1.139 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2431 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHENIX phasing