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Minimal diadenylate cyclase from E. coli PanDA immune system - IEX
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, HANGING DROP 295.15 0.1M HEPES sodium salt pH 7.5, 1.5M lithium sulfate at 7 mg/mL and were cryoprotected with addition of 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.97 58.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.159 α = 90 b = 67.32 β = 90 c = 173.278 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 2M 2026-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00006 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.99 43.84 100 0.022 19.5 13.3 54742 41.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.04 100 0.328 2.4 11.9
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 1.99 43.84 1.35 54742 1995 99.95 0.1926 0.1912 0.1926 0.2296 0.2291 61.75
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 21.9009 f_angle_d 1.7194 f_chiral_restr 0.1111 f_bond_d 0.0154 f_plane_restr 0.0117
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4569 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 109
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing