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A heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L28Y.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other model helices
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 After 1:1 dilution with the peptide solution, the resulting conditions were 50 mM sodium 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonate (sodium HEPES), 5% w/v PEG 8000 and 4% v/v ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.539 α = 90 b = 130.416 β = 90 c = 38.454 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 2018-01-22 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) 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 1.19 45.58 98.5 0.043 0.046 0.013 0.997 18 10.7 78107 17.62
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 1.19 1.22 91.2 0.893 0.982 0.397 0.723 1.6 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT model helices 1.19 45.53 71552 3764 94.82 0.1692 0.1675 0.1692 0.2039 0.2098 RANDOM 28.718
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] 1.17 -1.86 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.445 r_dihedral_angle_3_deg 14.212 r_rigid_bond_restr 5.975 r_dihedral_angle_1_deg 3.612 r_angle_refined_deg 1.847 r_angle_other_deg 1.675 r_chiral_restr 0.126 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.445 r_dihedral_angle_3_deg 14.212 r_rigid_bond_restr 5.975 r_dihedral_angle_1_deg 3.612 r_angle_refined_deg 1.847 r_angle_other_deg 1.675 r_chiral_restr 0.126 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1614 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling xia2 data scaling PHASER phasing