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Crystal structure of the human RAGE ectodomain in complex with murine S100A6 mutant Y84C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P2Y WT complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 9% isopropanol
Crystal Properties Matthews coefficient Solvent content 3.48 64.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.65 α = 90 b = 113.01 β = 90 c = 139.51 γ = 90
Symmetry Space Group I 2 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 PILATUS3 6M 2022-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.35 50 99.1 0.081 15.37 6.4 25103 47.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.42 100 0.884 2.1 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.35 43.907 1.36 25097 1267 99.13 0.2059 0.2043 0.212 0.2352 0.2389
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 18.235 f_angle_d 0.639 f_chiral_restr 0.066 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2977 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction