☰ Navigation Tabs
Deglycosylated Nogo Receptor with native disulfide structure 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Co-crystallization trial with mouse Nogo54, an extracellular construct derived from the NgR ligand Nogo-A (UNIPROT Q99P72, residues 1025-1078). Nogo54 was purified in 150 mM NaCl, 20 mM HEPES pH 7.0 at a concentration of 3.3 mg/mL and mixed in a 1:1 molar ratio with Endo-Hf-deglycosylated NgRa at a concentration of 10 mg/mL. Crystals were grown in a condition of 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG3350.
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.63 α = 90 b = 90.63 β = 90 c = 45.62 γ = 90
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 PILATUS 6M-F 2014-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.5 90.63 100 0.066 0.998 13.2 7.4 13084
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.61 100 0.912 0.704 2.4 7.6
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 1OZN 2.5 90.63 1.35 13057 650 99.86 0.2201 0.2186 0.2257 0.2479 0.252
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 19.4 f_angle_d 1.123 f_chiral_restr 0.052 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2419 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 152
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing