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Vanadate-bound Putative Ancestral Protein Tyrosine Phosphatase ShufPTP - Highest p-loop Conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 298.15 8 mg/mL protein, 0.1 M CAPS, 30% PEG 400, 5 mM sodium metavanadate at a 1:1:0.2 protein/well/additive screen. The additive screen contains 0.2 M (NH4)2SO4, 20-30% PEG 4000, and 10-35% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.04 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.05 α = 90 b = 86.05 β = 90 c = 32.225 γ = 120
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 6M 2021-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 50 99.1 0.168 0.173 0.039 1 9.1 16.8 12747 25.47
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 1.8 1.86 91.9 0.641 0.688 0.23 0.743 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 37.26 1.35 12709 641 98.92 0.1799 0.1781 0.1779 0.2138 0.2136 26.8
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 16.3031 f_angle_d 1.0082 f_chiral_restr 0.0627 f_plane_restr 0.0084 f_bond_d 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1221 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data scaling HKL-3000 data reduction PHASER phasing