☰ Navigation Tabs
Structure of the EC2 domain of CD9 in complex with nanobody 4E8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Structure of CD9EC2 bound to nanobody 4C8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.2 M sodium acetate, 0.1 M Tris pH 8.0, 30% (w/v) PEG 4,000
cryoprotected with reservoir solution supplemented with 20% (v/v) ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 1.91 35.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.521 α = 90 b = 89.446 β = 90 c = 35.684 γ = 90
Symmetry Space Group P 21 21 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 2019-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.33 44.72 92 0.04 0.02 1 17.6 6.4 32044 19.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.44 68.9 0.98 0.6 0.653 1.5 6.1
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 Structure of CD9EC2 bound to nanobody 4C8 1.33 44.72 1.35 32042 1570 69.74 0.1531 0.1512 0.1551 0.1898 0.1927 27.7
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 23.8579 f_angle_d 0.9406 f_chiral_restr 0.0772 f_bond_d 0.0079 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1570 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PHASER phasing