2024-01-17 REL RCSB RCSB RCSB 2021-12-21 2022-07-06 2022-07-06 2024-01-17 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM142495 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R00GM121856 C1-symmetric single-particle cryo-EM map of T. vaginalis FDPF3 Bell TA Chao LH oxygen scavenging, fmn, nadh, flavodiiron protein, OXIDOREDUCTASE Abdulaziz EN Bell TA Rashid B Heacock ML Begic T Skinner OS Yaseen MA Chao LH Mootha VK Pierik AJ Cracan V A natural fusion of flavodiiron, rubredoxin, and rubredoxin oxidoreductase domains is a self-sufficient water-forming oxidase of Trichomonas vaginalis. J.Biol.Chem. US 298 102210 102210 2022 35780837 doi:10.1016/j.jbc.2022.102210 1083-351X 0071 JBCHA3 EMD-25787 other EM volume
C2-symmetric map from same input particle set
 Dimeric assembly of TvFDPF3 N-terminal FDP-like domains Dimeric assembly of TvFDPF3 N-terminal FDP-like domains 0
Resolved portion of full-lengh TvFDPF3
Trichomonas vaginalis C-1:NIH singleParticle particle 0.8 7.5 50.0 HEPES 150.0 NaCl Sodium Chloride Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY 12.0 GLOW DISCHARGE AIR 3.9 ETHANE 100 295 FEI VITROBOT MARK IV
Blotting condition: 5 s at +15 blotting force..
Monodisperse sample
 FEI TITAN KRIOS OTHER OTHER FIELD EMISSION GUN 300 1.3 2.5 105000.0 GATAN K3 (6k x 4k) 1 7398 54.5
Images were collected as 51-frame movies.
 1 1511632
All micrographs were imported into CryoSPARC and preprocessed using the CryoSPARC internal Patch Motion Correction and Patch CTF Estimation jobs. An initial particle set was generated by blob picking particles between 80 and 180 angstroms in diameter from all micrographs. These particles were twice sequentially subjected to 2D classification, and the best classes selected. The micrographs were then manually curated to remove images with minimum CTF fits of 9 angstrom or greater. After curation, 6,938 of the original 7,398 movies remained under consideration. The 2D classes selected from blob picking were used to train a Topaz model, and the model was used to pick particles from the curated micrographs. Duplicate particles were removed by excluding particles with a center within 125 angstrom of another particle.
Model generated ab initio in RELION
 2 C1 6.6 FSC 0.143 CUT-OFF RELION 3.1.3 101628 MAXIMUM LIKELIHOOD RELION 3.1.3 MAXIMUM LIKELIHOOD RELION 3.1.3 6 RELION 3.1.3 emd_25790.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.2 211.2 211.2 90.0 90.0 90.0 X Y Z -0.042410154 0.06062507 0.00012107029 0.0018237053 0.825 0.825 0.825 0.013 AUTHOR Sharpened and masked C1-symmetric single-particle cryo-EM map of T. vaginalis FDPF3. This map has not had handedness inverted, as is shown in publication. emd_25790_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.2 211.2 211.2 90.0 90.0 90.0 X Y Z -0.042410154 0.06062507 0.000029343139 0.0027877993 0.825 0.825 0.825 AUTHOR Sharpened, unmasked C1-symmetric single-particle cryo-EM map of T. vaginalis FDPF3. This map has not had handedness inverted, as is shown in publication. emd_25790_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.2 211.2 211.2 90.0 90.0 90.0 X Y Z -0.012502142 0.021946121 0.000032095286 0.0012046377 0.825 0.825 0.825 AUTHOR Half-class 1 from refinement prior to sharpening. This map has not had handedness inverted, as is shown in publication. emd_25790_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 211.2 211.2 211.2 90.0 90.0 90.0 X Y Z -0.010743526 0.02327341 0.000026590968 0.0011970793 0.825 0.825 0.825 AUTHOR Half-class 2 from refinement prior to sharpening. This map has not had handedness inverted, as is shown in publication.