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Chroococcidiopsis thermalis Argonaute (CtAgo) bound to the 3' end of a guide DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Partial Alphafold model of CtAgo was used for phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein solution:
-3.74 mg/ml CtAgo
-500 mM KCl
-20 mM HEPES-KOH pH7.5
-1 mM DTT
Reservoir solution:
-0.05 M Ammonium Formate
-8% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.901 α = 90 b = 50.59 β = 102.75 c = 98.572 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 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 SLS X06SA
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 2.4 48.07 99 0.085 1 12.06 4 28341 63.08
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 2.4 2.49 1.467 0.771 0.96
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 2.4 48.07 1.34 28267 1413 99.01 0.2236 0.2218 0.2229 0.2575 0.2579 75.1
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 18.3022 f_angle_d 0.7576 f_chiral_restr 0.0475 f_plane_restr 0.0061 f_bond_d 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5487 Nucleic Acid Atoms 82 Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX refinement PHASER phasing Coot model building