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Crystal structure of the asgard SNARE-like domain from Candidatus Heimdallarchaeota archaeon B3-JM-08
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NPS Chain D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293.15 H6 BCS
Crystal Properties Matthews coefficient Solvent content 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.193 α = 90 b = 34.193 β = 90 c = 260.427 γ = 90
Symmetry Space Group I 4 2 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 2M 2022-02-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99999 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.4 50 99.9 0.999 21.81 11.5 5795 31.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.55 99.9 0.978 6.9 11.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 32.55 1.36 5782 292 99.74 0.2617 0.2611 0.2617 0.2738 0.2747 49.57
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 4.2624 f_angle_d 1.3359 f_chiral_restr 0.0548 f_bond_d 0.0147 f_plane_restr 0.0098
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 466 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX phasing PHENIX model building Coot model building PHENIX refinement