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Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URL 1URL, 4FRW, 1CS6 experimental model PDB 4FRW 1URL, 4FRW, 1CS6 experimental model PDB 1CS6 1URL, 4FRW, 1CS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.605 α = 71.86 b = 60.115 β = 86.51 c = 79.471 γ = 82.95
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 2014-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99998 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 56.79 97.5 0.157 0.985 5.9 4.5 32993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 95.7 0.981 0.565 1.6 4.3
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 2.3 56.786 1.96 32887 1639 97.23 0.2253 0.2238 0.2287 0.2541 0.2544 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 12.339 f_angle_d 0.583 f_chiral_restr 0.026 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4785 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 276
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing