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Crystal structure of the gasdermin-like protein RCD-1-1 from Neurospora crassa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQ6 in silico model AlphaFold AF-Q7SBA0-F1 AlphaFold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291 0.1 M Bicine pH 7.4, 11% PEG 3350, 3% (w/v) D(+)-Glucose monohydrate
Crystal Properties Matthews coefficient Solvent content 2.78 55.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.144 α = 90 b = 91.911 β = 101.38 c = 105.868 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 PILATUS3 6M 2022-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.35 79.55 99.9 0.09 0.098 0.037 0.998 12.3 6.8 63588 45.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 100 0.82 0.886 0.465 0.881 2.2 6.9
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 2.35 45.96 1.34 63475 2000 99.76 0.2175 0.2165 0.2175 0.2481 0.2478 58.05
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 11.3535 f_angle_d 0.4602 f_chiral_restr 0.1826 f_plane_restr 0.0031 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8741 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing