Cryo-EM Sample Prep:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
Microscopy:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
Transmission Electron Microscopy:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
Software:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
Biomarker Discovery:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
Inhibition:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
In Vitro:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
Activity Assay:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
CRISPR:Article Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Article Snippet: .. Csy:AcrIF24 1:5 Supplementary Table 3 Cryo-EM data collection and model refinement Csy-AcrIF24 (EMD- 31185, PDB 7ELM) Csy-AcrIF24-dsDNASP (EMD-31186, PDB 7ELN) Csy-AcrIF24-dsDNANS (EMD-32440, PDB 7WE6) Data collection and processing Microscope Tian Krios TEM (Thermo Fisher) Camera Gatan K3 Summit direct electron detector Energy filter Gatan GIF Quantum, 20eV slit Magnification (calibrated) 81,000 × Voltage 300 kV Defocus range (μm) -1.3 - -2.3 Total electron exposure (e-/Å2) 50 Exposure rate (e-/pixel/sec) 20 Pixel size (Å) 1.0742 1.1 Reconstruction Software RELION Micrographs used 2,374 2,793 4,294 Total extracted particles 1,122,799 933,567 1,079,487 Total refined particles 150,969 188,384 474,421 Symmetry applied C1 Map resolution (Å, FSC=0.143) 2.88 3.02 3.20 Local resolution range (Å) 2.4-4.0 Real space refinement Software phenix_real_space_refine in the PHENIX Model resolution (Å, FSC=0.5) 3.07 3.19 3.50 Model composition Non-hydrogen atoms 47399 48906 48325 Protein residues 6201 6209 6209 DNA/RNA 120 172 164 CC (box) 0.85 0.86 0.85 B factor of protein residues (mean) 66.09 78.97 150.12 B factor of nucleotide (mean) 138.93 212.26 216.33 R.M.S deviations Bond lengths (Å) 0.005 0.007 0.007 Bond angles (Å) 0.772 0.826 0.908 Validation Molprobity Score 1.76 1.74 2.39 Clashscore 6.36 6.53 6.53 Rotamer outliers (%) 0.40 0.58 5.94 C-beta deviations 0 0 0 CaBLAM outliers (%) 3.76 3.39 3.88 Ramachandran plot statics Favored (%) 93.91 94.39 93.23 Allowed (%) 6.05 5.54 6.76 Outliers (%) 0.03 0.06 0.02 Supplementary Fig. 1 Inhibition of AcrIF24 and AcrIF24ΔMD on the in vitro cleavage activity of type I-F CRISPR-Cas system. ..
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