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Crystal structure of human STEP (PTPN5) at cryogenic temperature (100 K) and ambient pressure (0.1 MPa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.65 293.15 30% PEG 3350, 200 mM Li2SO4, 100 mM bis-tris pH 5.65
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.666 α = 90 b = 63.508 β = 90 c = 135.156 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 S 16M 2020-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 1.033 CHESS 7B2
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 1.71 67.58 98.64 0.108 0.1222 0.05539 0.96 10.23 4.7 37552 29.03
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 1.711 1.772 93.42 2.37 2.621 1.106 0.374 0.59 4.8
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 1.71 67.58 1.33 37271 1862 98.63 0.1932 0.1915 0.1923 0.2244 0.2234 38.06
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 7.0847 f_angle_d 1.2039 f_chiral_restr 0.0636 f_bond_d 0.0127 f_plane_restr 0.0126
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2281 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement xia2 data scaling DIMPLE data reduction DIMPLE phasing