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Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MBS 4MBS, 1F2L, 3ONA, 4B41 experimental model PDB 1F2L 4MBS, 1F2L, 3ONA, 4B41 experimental model PDB 3ONA 4MBS, 1F2L, 3ONA, 4B41 experimental model PDB 4B41 4MBS, 1F2L, 3ONA, 4B41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.3 293 PEG 300, MES, sodium succinate, polypropylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.024 α = 90 b = 81.024 β = 90 c = 231.303 γ = 90
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 MARMOSAIC 300 mm CCD 2013-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.88 50 98.7 0.2 0.214 0.084 5.2 8.5 16648 58.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 2.93 74.8 0.524 0.304 6.8 629
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 4MBS, 1F2L, 3ONA, 4B41 2.886 38.234 1.35 16629 1659 99.57 0.2043 0.1991 0.2025 0.2492 0.2515 66.9984
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 12.801 f_angle_d 0.605 f_chiral_restr 0.021 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3700 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 255
Software Software Software Name Purpose HKL-2000 data reduction PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data scaling PHASER phasing