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Yorodumi- EMDB-38080: SIRM reconstruction of the MC-45 de novo processed ribosome 50S -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38080 | |||||||||
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Title | SIRM reconstruction of the MC-45 de novo processed ribosome 50S | |||||||||
Map data | The SIRM reconstructed ribosome 50S. The map was low-passed to 3.6 Angstrom. This map was reconstructed after Validation and Mask-Picking. | |||||||||
Sample |
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Keywords | ribosome 50S / RIBOSOME | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / Resolution: 3.6 Å | |||||||||
Authors | Zhang XZ / Zhu DJ / Cao WL | |||||||||
Funding support | China, 1 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Correction of preferred orientation-induced distortion in cryo-electron microscopy maps. Authors: Dongjie Zhu / Weili Cao / Junxi Li / Chunling Wu / Duanfang Cao / Xinzheng Zhang / Abstract: Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been ...Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been attempted to address this preferred orientation problem using tilt-collection strategy and modifications to grids or to air-water interfaces. However, these approaches often require time-consuming experiments, and the effect was always protein dependent. Here, we developed a procedure containing removing misaligned particles and an iterative reconstruction method based on signal-to-noise ratio of Fourier component to correct this distortion by recovering missing data using a purely computational algorithm. This procedure called signal-to-noise ratio iterative reconstruction method (SIRM) was applied on incomplete datasets of various proteins to fix distortion in cryo-EM maps and to a more isotropic resolution. In addition, SIRM provides a better reference map for further reconstruction refinements, resulting in an improved alignment, which ultimately improves map quality and benefits model building. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38080.map.gz | 20.3 MB | EMDB map data format | |
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Header (meta data) | emd-38080-v30.xml emd-38080.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_38080.png | 78.9 KB | ||
Masks | emd_38080_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-38080.cif.gz | 3.8 KB | ||
Others | emd_38080_half_map_1.map.gz emd_38080_half_map_2.map.gz | 172.3 MB 172.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38080 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38080 | HTTPS FTP |
-Validation report
Summary document | emd_38080_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_38080_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_38080_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_38080_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38080 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38080 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38080.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The SIRM reconstructed ribosome 50S. The map was low-passed to 3.6 Angstrom. This map was reconstructed after Validation and Mask-Picking. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.94666 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38080_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: These two unfil-maps were NOT reconstructed by SIRM....
File | emd_38080_half_map_1.map | ||||||||||||
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Annotation | These two unfil-maps were NOT reconstructed by SIRM. They were reconstructed by conventional relion_reconstruct, to generate a FSC curve. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: These two unfil-maps were NOT reconstructed by SIRM....
File | emd_38080_half_map_2.map | ||||||||||||
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Annotation | These two unfil-maps were NOT reconstructed by SIRM. They were reconstructed by conventional relion_reconstruct, to generate a FSC curve. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E. coli 70S ribosome, from EMPIAR-10509
Entire | Name: E. coli 70S ribosome, from EMPIAR-10509 |
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Components |
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-Supramolecule #1: E. coli 70S ribosome, from EMPIAR-10509
Supramolecule | Name: E. coli 70S ribosome, from EMPIAR-10509 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 Details: We used EMPIAR-10509. This repository was not recorded by us. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: RELION (ver. 3.1.2) / Software - details: SIRM-RELION Details: The map was low-passed to 3.6 Angstrom. The reported resolution was 3.1 Angstrom via FSC-0.143 (Gold-standard). Number images used: 28050 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2) |