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Myelin-associated glycoprotein (MAG) glycosylated and lysine-methylated full extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URL 1URL, 4FRW, 1CS6, 3P3Y, 2YD6 experimental model PDB 4FRW 1URL, 4FRW, 1CS6, 3P3Y, 2YD6 experimental model PDB 1CS6 1URL, 4FRW, 1CS6, 3P3Y, 2YD6 experimental model PDB 3P3Y 1URL, 4FRW, 1CS6, 3P3Y, 2YD6 experimental model PDB 2YD6 1URL, 4FRW, 1CS6, 3P3Y, 2YD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Crystals were grown from protein that was modified by reductive lysine methylation. Protein was concentrated to 8.4 mg/mL, which was mixed 1:1 with reservoir solution. Crystals grew in a condition containing 200 mM NaOAc and 20 % PEG3350 (w/v).
Crystal Properties Matthews coefficient Solvent content 7.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.237 α = 90 b = 101.237 β = 90 c = 687.477 γ = 120
Symmetry Space Group P 65 2 2
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 2013-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97553 PETRA III, EMBL c/o DESY P14 (MX2)
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 4.3 114.62 100 0.115 15.6 35.7 15430
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 4.3 4.81 100 3.937 1.3 36.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1URL, 4FRW, 1CS6, 3P3Y, 2YD6 4.3 114.579 1.34 15425 769 99.97 0.2859 0.2855 0.3074 0.2955 0.3189 Random selection
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 14.155 f_angle_d 1.331 f_chiral_restr 0.198 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3776 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 166
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing