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. 2022 Dec 12;29(12):1196–1207. doi: 10.1038/s41594-022-00863-y

Table 1.

Cryo-EM data collection, refinement, and validation statistics

LRRK2RCKW + MT +MLi-2 (Helical) LRRK2RCKW + MT + MLi-2 (Tetramer only)
EMDB-25649 EMDB-25664
EMPIAR-10925 EMPIAR-10925
Data collection and processing
Magnification 36,000 36,000
Voltage (kV) 200 200
Electron exposure (e–/Å2) 55 55
Defocus range (μm) 0.5–2.5 0.5–2.5
Pixel size (Å) 1.16 1.16
Symmetry imposed +32.5° rot, 33.3 Å rise C1
Initial particle images (no.) 354,271 206,649 (symmetry expanded)
Final particle images (no.) 14,350 133,246
Map resolution (Å) 18 5.9
 FSC threshold 0.143
Map resolution range (Å) N/A 3.5–9
Refinement
Initial model used (PDB code) N/A N/A
Model resolution (Å) N/A N/A
 FSC threshold
Model resolution range (Å) N/A N/A
Map sharpening B factor (Å2) N/A −339
Model composition N/A N/A
 Non-hydrogen atoms
 Protein residues
 Ligands
B factors (Å2) N/A N/A
 Protein
 Ligand
R.m.s. deviations N/A N/A
 Bond lengths (Å)
 Bond angles (°)
Validation N/A N/A
 MolProbity score
 Clashscore
 Poor rotamers (%)
Ramachandran plot N/A N/A
 Favored (%)
 Allowed (%)
 Disallowed (%)
LRRK2RCKW + MT + MLi-2 (tetramer + MT) LRRK2RCKW + MT + MLi-2 (microtubule only)
EMDB-25658 EMDB-25908
EMPIAR-10925 EMPIAR-10925
Data collection and processing
Magnification ×36,000 ×36,000
Voltage (kV) 200 200
Electron exposure (e–/Å2) 55 55
Defocus range (μm) 0.5–2.5 0.5–2.5
Pixel size (Å) 1.16 1.16
Symmetry imposed C1 C1
Initial particle images (no.) 206,649 (symmetry expanded) 206,649 (symmetry expanded)
Final particle images (no.) 133,246 133,246
Map resolution (Å) 6.6 5.4
 FSC threshold 0.143
Map resolution range (Å) 3.7–9.5 2.6–9.0
Refinement
Initial model used (PDB code) N/A N/A
Model resolution (Å) N/A N/A
 FSC threshold
Model resolution range (Å) N/A N/A
Map sharpening B factor (Å2) −326 −235
Model composition N/A N/A
 Non-hydrogen atoms
 Protein residues
 Ligands
B factors (Å2) N/A N/A
 Protein
 Ligand
R.m.s. deviations N/A N/A
 Bond lengths (Å)
 Bond angles (°)
Validation N/A N/A
 MolProbity score
 Clashscore
 Poor rotamers (%)
Ramachandran plot N/A N/A
 Favored (%)
 Allowed (%)
 Disallowed (%)
LRRK2RCKW + MT +MLi-2 (minus end) LRRK2RCKW + MT +MLi-2 (plus end)
EMDB-25674 EMDB-25672
EMPIAR-10924 EMPIAR-10921
PDB-7THY PDB-7THZ
Data collection and processing
Magnification ×36,000 ×36,000
Voltage (kV) 200 200
Electron exposure (e–/Å2) 55 55
Defocus range (μm) 0.5–2.5 1.2–1.8
Pixel size (Å) 1.16 1.16
Symmetry imposed C1 C1
Initial particle images (no.) 206,649 (symmetry expanded) 206,649 (symmetry expanded)
Final particle images (no.) 99,854 99,854
Map resolution (Å) 5.2 5.0
 FSC threshold 0.143
Map resolution range (Å) 2.6–9.0 2.9–7.0
Refinement
Initial model used (PDB code) Q5S007 (AlphaFold) Q5S007 (AlphaFold)
Model resolution (Å) 5.4 (average) 5.3 (average)
 Resolution method Q-score Q-score
Model resolution range (Å) 3.0–8.6 3.5–8.0
Map sharpening B factor (Å2) −200 −200
Model composition N/A N/A
 Non-hydrogen atoms
 Protein residues
 Ligands
B factors (Å2) N/A N/A
 Protein
 Ligand
R.m.s. deviations N/A N/A
 Bond lengths (Å)
 Bond angles (°)
Validation N/A N/A
 MolProbity score
 Clashscore
 Poor rotamers (%)
Ramachandran plot N/A N/A
 Favored (%)
 Allowed (%)
 Disallowed (%)
LRRK2RCKW + MT +MLi-2 (focused on kinase)
EMDB-25897
EMPIAR-10925
Data collection and processing
Magnification 36,000
Voltage (kV) 200
Electron exposure (e–/Å2) 55
Defocus range (μm) 0.5–2.5
Pixel size (Å) 1.16
Symmetry imposed C1
Initial particle images (no.) 206,649 (symmetry expanded)
Final particle images (no.) 133,246
Map resolution (Å) 4.5
 FSC threshold 0.143
Map resolution range (Å) 3.0–8.0
Refinement
Initial model used (PDB code) N/A
Model resolution (Å) N/A
 FSC threshold
Model resolution range (Å) N/A
Map sharpening B factor (Å2) −146
Model composition N/A
 Non-hydrogen atoms
 Protein residues
 Ligands
B factors (Å2) N/A
 Protein
 Ligand
R.m.s. deviations N/A
 Bond lengths (Å)
 Bond angles (°)
Validation N/A
 MolProbity score
 Clashscore
 Poor rotamers (%)
Ramachandran plot N/A
 Favored (%)
 Allowed (%)
 Disallowed (%)
LRRK2RCKW + MT +MLi-2 (minus end) LRRK2RCKW + MT +MLi-2 (plus end)
EMDB-25674 EMDB-25672
EMPIAR-10924 EMPIAR-10921
PDB-7THY PDB-7THZ
Data collection and processing
Magnification 36,000 36,000
Voltage (kV) 200 200
Electron exposure (e–/Å2) 55 55
Defocus range (μm) 0.5–2.5 1.2–1.8
Pixel size (Å) 1.16 1.16
Symmetry imposed C1 C1
Initial particle images (no.) 206,649 (symmetry expanded) 206,649 (symmetry expanded)
Final particle images (no.) 99,854 99,854
Map resolution (Å) 5.2 5.0
 FSC threshold 0.143
Map resolution range (Å) 2.6–9.0 2.9–7.0
Refinement
Initial model used (PDB code) Q5S007 (AlphaFold) Q5S007 (AlphaFold)
Model resolution (Å) 5.4 (average) 5.3 (average)
 Resolution method Q-score Q-score
Model resolution range (Å) 3.0-8.6 3.5-8.0
Map sharpening B factor (Å2) −200 −200
Model composition
 Non-hydrogen atoms 1012 1012
 Protein residues 194 194
 Ligands 1 1
B factors (Å2)
 Protein −219 (average) −216 (average)
 Ligand N/A N/A
R.m.s. deviations
 Bond lengths (Å) 0.019 (average) 0.020 (average)
 Bond angles (°) 1.907 (average) 2.023 (average)
Validation
 MolProbity score 1.49 (average) 1.54 (average)
 Clashscore 3.52 (average) 3.96 (average)
 Poor rotamers (%) 0 (average) 0 (average)
Ramachandran plot
 Favored (%) 94.5 (average) 94.6 (average)
 Allowed (%) 4.9 (average) 4.8 (average)
 Disallowed (%) 0.6 (average) 0.6 (average)