[English] 日本語
![](img/lk-miru.gif)
- EMDB-7550: Rabbit muscle aldolase at 2.4A resolution (17dec27a 205k particle... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-7550 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Rabbit muscle aldolase at 2.4A resolution (17dec27a 205k particles, all images) | |||||||||
![]() | rabbit muscle aldolase at 2.4 A resolution (17dec27a <25nm ice thickness) | |||||||||
![]() |
| |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
![]() | Kim LK / Rice WJ / Eng ET / Kopylov M / Cheng A / Raczkowski AM / Jordan KD / Bobe D / Potter CS / Carragher B | |||||||||
![]() | ![]() Title: Benchmarking cryo-EM Single Particle Analysis Workflow. Authors: Laura Y Kim / William J Rice / Edward T Eng / Mykhailo Kopylov / Anchi Cheng / Ashleigh M Raczkowski / Kelsey D Jordan / Daija Bobe / Clinton S Potter / Bridget Carragher / ![]() Abstract: Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software ...Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software components of their single particle analysis workflow. The workflow is complex, with many bottlenecks existing at the specimen preparation, data collection and image analysis steps; the samples and grid preparation can be of unpredictable quality, there are many different protocols for microscope and camera settings, and there is a myriad of software programs for analysis that can depend on dozens of settings chosen by the user. For this reason, we believe it is important to benchmark the entire workflow, using a standard sample and standard operating procedures, on a regular basis. This provides confidence that all aspects of the pipeline are capable of producing maps to high resolution. Here we describe benchmarking procedures using a test sample, rabbit muscle aldolase. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 14.1 KB 14.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 43.9 KB | ||
Others | ![]() ![]() | 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7528C ![]() 7541C ![]() 7551C ![]() 7562C ![]() 7614C ![]() 7615C ![]() 7616C ![]() 7617C C: citing same article ( |
---|---|
Similar structure data | |
EM raw data | ![]() Data size: 85.6 Data #1: aligned micrographs of rabbit muscle aldolase from 17dec27a [micrographs - multiframe]) |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | rabbit muscle aldolase at 2.4 A resolution (17dec27a <25nm ice thickness) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: rabbit muscle aldolase at 2.4 A resolution (17dec27a...
File | emd_7550_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | rabbit muscle aldolase at 2.4 A resolution (17dec27a <25nm ice thickness), half-map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: rabbit muscle aldolase at 2.4 A resolution (17dec27a...
File | emd_7550_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | rabbit muscle aldolase at 2.4 A resolution (17dec27a <25nm ice thickness), half-map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Rabbit muscle aldolase
Entire | Name: Rabbit muscle aldolase |
---|---|
Components |
|
-Supramolecule #1: Rabbit muscle aldolase
Supramolecule | Name: Rabbit muscle aldolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Experimental: 150 KDa |
-Macromolecule #1: rabbit muscle aldolase
Macromolecule | Name: rabbit muscle aldolase / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO / EC number: fructose-bisphosphate aldolase |
---|---|
Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAAWRC VLKIGEHTPS A LAIMENAN ...String: PHSHPALTPE QKKELSDIAH RIVAPGKGIL AADESTGSIA KRLQSIGTEN TEENRRFYRQ LLLTADDRVN PCIGGVILFH ETLYQKADD GRPFPQVIKS KGGVVGIKVD KGVVPLAGTN GETTTQGLDG LSERCAQYKK DGADFAAWRC VLKIGEHTPS A LAIMENAN VLARYASICQ QNGIVPIVEP EILPDGDHDL KRCQYVTEKV LAAVYKALSD HHIYLEGTLL KPNMVTPGHA CT QKYSHEE IAMATVTALR RTVPPAVTGV TFLSGGQSEE EASINLNAIN KCPLLKPWAL TFSYGRALQA SALKAWGGKK ENL KAAQEE YVKRALANSL ACQGKYTPSG QAGAAASESL FISNHAY |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |