EMDB Validation Analysis : EMD-43484

EMD-43484 › Validation analysis

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Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and chloramphenicol:50S-HflX-A-Clm

Validation summary

Resolution:
Method:
Map released:
Last modified:
Sample name:
3.33 Å (depositor provided) (FSC 0.143 CUT-OFF)
Single particle reconstruction
2025-02-19
2025-02-19
Mycobacterium smegmatis 50S ribosome bound to HflX-GMPPCP complex and Chloramphenicol
Organism:
Fitted atomic model:
Mycolicibacterium smegmatis MC2 155
8vrl (32 chains, 96136 atoms)

Model evaluation bars:

Model Metric Evaluation bar Average value
8vrl Q-score
0.495
Atom Inclusion
0.827
CCC
0.786
SMOC
0.725

Additional validation information

Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-43484) and model-map (8vrl and EMD-43484). Validation analysis of this entry is available in the main page. Documentation for the outputs of EMDB Validation Analysis can be found on the help page.

Map parameters

Recommended contour level:
Number of grid points:
Voxel size:
Minimum value:
Maximum value:
Average value:
Standard deviation:
0.17
512 × 512 × 512
0.844 × 0.844 × 0.844 Å
-0.931
1.438
0.002
0.053
Image not available

Primary map visualisation

Projections

Raw map visualisation (Raw map calculated from deposited two half-maps)

Volume graphs
Download: EMDB Mask Learn more EMDB Raw Map Learn more Depositor Half Map 1 Depositor Half Map 2
Map resolution (Å) measured by Fourier Shell Correlation (FSC)
EMDB calculated FSC Author FSC
Threshold Unmasked Masked Corrected Author
FSC 0.143 4.19 3.47 3.46 3.33
FSC 0.5 8.09 3.87 3.87 3.59
FSC half-bit 4.33 3.50 3.50 3.35

Map and 1 fitted model

Map with model 8vrl (Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and chloramphenicol:50S-HflX-A-Clm)
Primary map with model views
Title
X projection

X

Y projection

Y

Z projection

Z

Map-model fit plots
Chain scores summary
Strudel Information
Chain:
Score range:

EMDB generated mask(s)

FSC mask with raw map
Title
X projection

X

Y projection

Y

Z projection

Z

Symmetry Information
No rotational symmetry has been detected in this map.