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Structure of a 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 experimental model PDB 1F2L 4MBS, 1F2L, 3ONA experimental model PDB 3ONA 4MBS, 1F2L, 3ONA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7.4 293 PEG 300, HEPES, ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.9 α = 90 b = 192.7 β = 90 c = 94.4 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 6M 2014-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.8 48.92 85 0.275 4.1 5.6 4834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 3.937 55.5 0.555 1.6 2.9
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 4MBS, 1F2L, 3ONA 3.801 48.92 1.35 4827 484 84.94 0.2878 0.2835 0.2892 0.3221 0.329 random selection
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 11.365 f_angle_d 0.874 f_chiral_restr 0.031 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2718 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing