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Protein with novel 3_1 knotted solenoid 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 0.1M Sodium acetate (pH 4.5),
0.2M Li2SO4, 30%w/v PEG8000,
protein solution 10 mg/ml in 50 mM Tris, 200 mM NaCl, 5% glycerol, ph 8 (at 277 K)
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.69 α = 90 b = 57.69 β = 90 c = 70.49 γ = 120
Symmetry Space Group P 31 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 EIGER X 16M 2024-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97624 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 1.22 40.76 100 0.082 1 13.78 9.86 40919 19.32
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 1.22 1.29 100 1.583 0.567 1.22 9.54
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 1.22 28.85 1.34 40915 1996 99.97 0.1312 0.1299 0.1299 0.1562 0.1285 20.66
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 11.9588 f_angle_d 1.1074 f_chiral_restr 0.0874 f_plane_restr 0.0176 f_bond_d 0.0106
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 986 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 49
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XDS data scaling PHASER phasing PHENIX refinement PHENIX model building Coot model building