Table 2 Cryo-EM data collection, refinement and validation statistics

From: High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase

Dataset	OdhA	OdhA-CoASH	OdhA-succinyl-CoA	OdhA-SP	OdhA-OdhI
Data collection and processing
Grid type	UltrAuFoil300 mesh R1.2/1.3	UltrAuFoil300 mesh R1.2/1.3	UltrAuFoil300 mesh R1.2/1.3	Lacey 200mesh	Lacey 200mesh
Plunge freezer	Vitrobot	Vitrobot	Vitrobot	Vitrobot	Vitrobot
Microscope	Krios	Krios	Krios	Krios	Krios
Magnification	105000	105000	105000	105000	105000
Voltage (kV)	300	300	300	300	300
Energy filter(eV)	20	20	20	20	20
Camera	K3	K3	K3	K3	K3
Detector mode	Counted	Counted	Super-resolution	Counted	Counted
Electron exposure (e–/Å²)	40	40	48	40	40
Defocus range (μm)	−0.8 to −2.0	−0.8 to −2.0	−0.8 to −2.0	−0.8 to −2.2	−0.8 to −2.2
Pixel size (Å)	0.86	0.86	0.84	0.86	0.86
Micrographs	13348	12202	11827	16647	19443
No. of fractions	40	40	50	60	40
Symmetry imposed	D3	D3	D3	D3	D3
Initial particle images (no.)	6571029	3392043	3827956	2599031	3177955
Final particle images (no.)	1474608	1849406	1074837	646352	958690
Map resolution (Å)^a	2.17	2.17	2.07	2.26	2.29
FSC threshold	0.143	0.143	0.143	0.143	0.143
Map resolution range (Å)	1.9–4.4	1.9–4.5	1.9–4.7	2.0–4.6	2.0–6.0
Refinement and validation
Model-map resolution (Å)^b	2.3	2.2	2.2	2.3	2.3
FSC threshold	0.5	0.5	0.5	0.5	0.5
Map sharpening B factor (Å²)	−84.4	−88.5	−74.2	−87.3	−93.3
Model composition
No. Atoms (non-H)	52590	52878	54248	52656	55346
Protein residues	6714	6714	6726	6714	7110
Ligands	18	24	24	18	12
Water molecules	–	–	1280	–	–
Average B factors (Å²)
Protein	45.28	43.41	67.11	45.07	47.22
Ligands	56.18	57.52	83.72	56.28	123.89
R.m.s. deviations^b
Bond lengths (Å)	0.010	0.010	0.006	0.008	0.013
Bond angles (°)	1.247	1.229	1.032	1.121	1.810
Validation^b
MolProbity score	1.00	1.02	1.08	0.88	0.90
Clashscore	1.05	1.25	1.82	0.77	0.66
Poor rotamers (%)	0.42	0.31	0.53	0.11	0.21
Ramachandran plot^b
Favored (%)	96.82	97.02	97.26	97.24	96.87
Allowed (%)	3.18	2.97	2.74	2.67	3.13
Outliers (%)	0.00	0.01	0.00	0.09	0.00
PDB accession code	8P5T	8P5U	8P5V	8P5W	8P5X
EMDB accession code	EMD-17452	EMD-17453	EMD-17454	EMD-17455	EMD-17456

^aResolution estimates from cryoSPARC (version v3.2.0)⁶¹.
^bValues from MOLPROBITY⁵⁸ and the PHENIX⁵⁹ EM validation tools.

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Table 2 Cryo-EM data collection, refinement and validation statistics

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