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Protein Tyrosine Phosphatase 1B F135Y mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 100 mM HEPES, 200 mM magnesium acetate, and 14% polyethylene glycol 8000, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.16 66.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.197 α = 90 b = 89.197 β = 90 c = 105.734 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 CCD ADSC QUANTUM 315r 2017-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.08 77.25 100 0.101 0.033 0.999 14.4 10.5 29715
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.12 2.08 0.655 0.72
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3A5J 2.08 77.25 27169 1362 95.98 0.25645 0.25472 0.2594 0.29122 0.3071 RANDOM 45.536
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] -0.6 -0.3 -0.6 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.037 r_dihedral_angle_4_deg 16.821 r_dihedral_angle_3_deg 14.648 r_long_range_B_other 10.523 r_long_range_B_refined 10.519 r_scangle_other 8.105 r_scbond_it 6.49 r_scbond_other 6.485 r_dihedral_angle_1_deg 5.727 r_mcangle_it 5.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.037 r_dihedral_angle_4_deg 16.821 r_dihedral_angle_3_deg 14.648 r_long_range_B_other 10.523 r_long_range_B_refined 10.519 r_scangle_other 8.105 r_scbond_it 6.49 r_scbond_other 6.485 r_dihedral_angle_1_deg 5.727 r_mcangle_it 5.437 r_mcangle_other 5.435 r_mcbond_it 4.405 r_mcbond_other 4.364 r_angle_refined_deg 1.046 r_angle_other_deg 0.715 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 1
Software Software Software Name Purpose DIALS data collection xia2 data reduction xia2 data scaling PHASER phasing PHENIX refinement