☰ Navigation Tabs
STEP (PTPN5) at high resolution with citrate bound in active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 2 VAPOR DIFFUSION, SITTING DROP 5.65 298.15 30% PEG 3350, 120 mM lithium citrate, 100 mM bis-tris pH 5.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.105 α = 90 b = 64.154 β = 90 c = 136.043 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 XE 9M 2021-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97946 NSLS-II 19-ID
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 1.27 58.03 99.9 0.157 0.163 0.046 0.998 9.2 12.5 93644 12.41
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 1.27 1.29 99 4.132 4.313 1.217 0.364 1.1 12.2
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 1.27 37.03 1.34 93488 4679 99.7 0.1318 0.1306 0.1323 0.1533 0.1545 22.84
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 13.4116 f_angle_d 0.9635 f_chiral_restr 0.0786 f_plane_restr 0.0091 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2281 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing