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Crystal structure of designed heterotrimeric assembly DHT03_1arm_A21/B/C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other de novo designed DHT03_1arm_A21/B/C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277.15 1M LiCl, 0.1M Sodium citrate pH5, 20% (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.31 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.73 α = 73.422 b = 73.5 β = 82.919 c = 97.28 γ = 80.781
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 EIGER X 16M 2020-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033167 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.35 49.01 84.33 0.07623 0.07623 0.1078 0.0762 0.998 6.88 1.9 19545 94.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.35 3.47 71.67 0.7649 0.7649 1.082 0.7645 0.431 1.01 1.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE de novo designed DHT03_1arm_A21/B/C 3.35 49.01 0.02 17649 1772 84.35 0.2547 0.2491 0.249 0.3051 0.3048 98.69
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 9.6273 f_angle_d 0.3614 f_chiral_restr 0.0283 f_plane_restr 0.0033 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11020 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement Coot model building