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X-ray crystal structure of a de novo designed single-chain parallel coiled-coil alpha-helical barrel with 5 inner helices, sc-CC-5-24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 JCSG+ D2: 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES, pH 7.5, 30 % v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 1.89 34.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.981 α = 90 b = 41.359 β = 104.6 c = 62.556 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER2 XE 16M 2023-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
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 1.9 60.54 99.83 0.05919 0.06239 0.01955 0.999 20.16 10.1 18195 35.71
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 1.9 1.968 99.78 0.4768 0.5075 0.1717 0.935 1.93 8.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 60.54 1.37 18174 895 99.73 0.1887 0.1873 0.2154 0.2163
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 3.444 f_angle_d 0.443 f_chiral_restr 0.033 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1924 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement xia2.multiplex data reduction xia2.multiplex data scaling PHASER phasing