☰ Navigation Tabs
Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Sigma
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YD4 PDB ENTRY 2YD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 0.2M AMMONIUM IODIDE, 20% W/V PEG 3350, PH 6.2 .
Crystal Properties Matthews coefficient Solvent content 2.38 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.4 α = 90 b = 29.49 β = 92.61 c = 61.58 γ = 90
Symmetry Space Group C 1 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 ASDC QUANTUM 4R M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.55 29 98.1 0.08 13.7 3.5 7438 -3 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.6 84.8 0.67 2.6 3.1
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2YD4 2.552 27.237 6759 322 89.24 0.1995 0.1962 0.1938 0.2602 0.2556 31.8
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] -7.183 -4.5739 -3.4048 -6.4729
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.321 f_angle_d 0.905 f_chiral_restr 0.061 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1524 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement xia2 data reduction XDS data reduction xia2 data scaling SCALA data scaling PHASER phasing