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Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LP5 4LP5, 1K96 experimental model PDB 1K96 4LP5, 1K96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol
Crystal Properties Matthews coefficient Solvent content 3.61 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.78 α = 90 b = 113.39 β = 90 c = 140.32 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 CCD MAR CCD 165 mm 2012-02-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.041 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 35 99.7 0.074 0.08 15.56 7 27554 2 -3 44.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 100 0.435 0.469 4.12 7.2
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 4LP5, 1K96 2.3 27.242 2 27064 1355 98 0.1877 0.1866 0.1942 0.2067 0.2157 random selection 52.48
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 14.74 f_angle_d 0.875 f_chiral_restr 0.059 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2974 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 42
Software Software Software Name Purpose XDS data scaling XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing PHENIX refinement