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Crystal structure of the 4th FN3 domain of human Protein Tyrosine phosphatase, receptor type F [PSI-NYSGRC-006240]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EDX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 298 Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol, Reservoir (0.2M Lithium Sulfate, 0.1M CAPS, 1.2M NaH2PO4/0.8M K2HPO4), Cryoprotection (2M Li2SO4), VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.9 35.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.011 α = 90 b = 39.677 β = 90 c = 68.525 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 CCD ADSC QUANTUM 315 MIRRORS 2013-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.456 34.337 94 8.1 16720
Refinement Statistics Diffraction ID Structure Solution 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 2EDX 1.456 34.337 1.34 16660 836 93.62 0.1641 0.1623 0.1674 0.1983 0.1985 24.7118
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 13.452 f_angle_d 1.233 f_chiral_restr 0.076 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 832 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 10
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction CBASS data collection XDS data reduction PHENIX phasing