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Crystal structure of human claudin-9 in complex with Clostridium perfringens entertoxin C-terminal domain in open form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AM2 Homology model and PDB entry 3AM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 150 mM sodium acetate, sodium cacodylate, Bis-Tris propane, pH 4.5, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 6.12 79.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.981 α = 90 b = 114.817 β = 90 c = 115.602 γ = 90
Symmetry Space Group P 21 21 21
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 S 6M 2017-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.2 70.98 100 0.127 0.139 0.056 0.999 3.9 6.1 16155 145.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.42 100 4.941 5.397 2.146 0.512 6.2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Homology model and PDB entry 3AM2 3.25 20.125 1.33 14613 2113 90.48 0.3013 0.3007 0.326 0.3077 0.3536 185.27
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 6.72 f_angle_d 0.958 f_chiral_restr 0.048 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2217 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing