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Protein with novel 8.3 knotted fold - EIGHT fold (Extraordinarily Intricate Globular Helical Tangled fold).
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 277 0.16 M calcium acetate, 0.08 M MES (pH 6.5), 14.4% w/v PEG 8000, protein solution 9 mg/ml in 50 mM MOPS, 200 mM NaCl, 5% glycerol (pH 6.5 at 277 K)
Crystal Properties Matthews coefficient Solvent content 3.7 66.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.13 α = 90 b = 94.34 β = 101.14 c = 120.85 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2026-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.54981 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.92 47.56 99.5 0.085 0.999 14.77 6.94 33597 86.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.92 3.1 99.6 0.837 0.814 2.05 7.12
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 2.92 47.17 1.39 33589 1678 99.57 0.2072 0.2052 0.2052 0.2426 0.2432 94.89
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 6.3041 f_angle_d 0.8357 f_chiral_restr 0.0449 f_plane_restr 0.0076 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6608 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction XDS data scaling PHASER phasing PHENIX model building Coot model building