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Structure of Cap9-CdnD complex containing NDG modification
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 8.5 291.15 0.1 M Tris-HCl pH 8.5, 24% PEG-3350, 5 mM MgCl2, 1 mM AMP
Crystal Properties Matthews coefficient Solvent content 2.19 43.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.664 α = 90 b = 58.219 β = 90 c = 89.228 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2025-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979 NSLS-II 17-ID-2
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 2.15 43.15 96.43 0.2997 0.3196 0.1096 0.993 6.32 8.2 25975 26.81
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 2.15 2.23 100 2.042 2.172 0.7334 0.378 8.5
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 2.15 43.15 1.34 25888 1359 96.43 0.2063 0.2048 0.2051 0.2317 0.2299 42.7
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 16.3129 f_angle_d 0.5654 f_chiral_restr 0.041 f_plane_restr 0.0055 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3472 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement AutoProcess data processing Coot model building XDS data reduction Aimless data scaling PHASER phasing