2020-01-29 REL RCSB RCSB RCSB 2017-06-30 2018-10-10 2018-10-10 2020-01-29 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM085043 United States 80S ribsome from Oryctolagus cuniculus, class I - with non-rotated/non-swiveled 40S and P site tRNA, derived from EMPIAR-10064 using eClarity Himes BA Zhang P Himes BA Zhang P Enhanced Macromolecular Classification and Alignment for High-resolution in Situ Tomography eLife US 2018 2050-084X EMD-3420 other EM volume
Map from the same data by the original authors using pyTOM for the image processing.
 EMD-8802 associated EM volume
Class I (of V)
 EMD-8803 other EM volume
Class II (of V)
 EMD-8804 other EM volume
Class III (of V)
 EMD-8805 other EM volume
Class IV (of V)
 EMD-8006 other EM volume
Class V (of V)
 80s ribsome from Oryctolagus cuniculus 80s ribsome from Oryctolagus cuniculus 0 Oryctolagus cuniculus Reticulocyte subtomogramAveraging particle 7.6 20.0 HEPES 50.0 KCl potassium chloride 2.0 MgCl2 magnesium chloride Quantifoil R2/1 COPPER PLASMA CLEANING ETHANE 60 295 FEI VITROBOT MARK IV
blot 3 seconds prior to plunging.
FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.0024 0.0037 Gatan Quantum
Data collection 20 --> -60, 22 --> 60 degrees
GATAN K2 SUMMIT (4k x 4k) INTEGRATING 3838 3710 1.5 1 1 C1 BACK PROJECTION 9.3 FSC 0.143 CUT-OFF emClarity 1.0 adapted single particle wiener filter
Independent beyond 3.6 nm as determined by the FSC at the time of dividing the half-sets
474 4 3090 emClarity 1.0 Included astigmatism and per-tilt CTF determination
Phases corrected on the projections by multiplying by the CTF in tiles compensating for the defocus gradient in tilted images.
 5 500 emClarity 1.0
3,090 total subtomograms were assigned to 5 separate classes using multi-scale PCA with full-3dCTF compensated estimators. 1.0,1.6,2.4,5.4 nm were the length-scales used for the msPCA.
 OTHER emClarity 1.0
3D refinement with two half-sets fully separated after template matching, at which point the FSC 0.5 was 3.6 nanometers. Reference and subtomograms filtered dynamically according to the FSC at each cycle using the FOM approach.
 emd_8802.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 336 336 336 0 0 0 336 336 336 880.31995 880.31995 880.31995 90.0 90.0 90.0 X Y Z -7.3996115 11.932767 0.010260821 0.2671052 2.62 2.62 2.62 2 AUTHOR Rabbit 80S ribosome derived from EMPIAR-10064 using emClarity. Non-rotated/non-swiveled 40S with P site tRNA.