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Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YD6 2YD6, 2YD9, 4DEP, 3O4O, 4YFE experimental model PDB 2YD9 2YD6, 2YD9, 4DEP, 3O4O, 4YFE experimental model PDB 4DEP 2YD6, 2YD9, 4DEP, 3O4O, 4YFE experimental model PDB 3O4O 2YD6, 2YD9, 4DEP, 3O4O, 4YFE experimental model PDB 4YFE 2YD6, 2YD9, 4DEP, 3O4O, 4YFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 15% PEG3350, 0.1 M ammonium sulfate and 0.1 M tri-sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.34 71.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.497 α = 90 b = 63.306 β = 94.23 c = 169.35 γ = 90
Symmetry Space Group P 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 RAYONIX MX225HE 2013-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.25 50 97.3 0.118 10.7 4.7 25436
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 3.25 3.31 92.5 0.438 2 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2YD6, 2YD9, 4DEP, 3O4O, 4YFE 3.253 48.974 1.44 25418 1292 97.04 0.2574 0.2558 0.2579 0.2867 0.2866
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 17.131 f_angle_d 1.149 f_chiral_restr 0.048 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6505 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing