EMDB Validation Analysis : EMD-11638

EMD-11638 › Validation analysis

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Cryo-EM structure of mouse heavy-chain apoferritin at 1.22 A

Validation summary

Resolution:
Method:
Map released:
Last modified:
Sample name:
1.22 Å (depositor provided) (FSC 0.143 CUT-OFF)
Single particle reconstruction
2020-10-28
2023-06-21
Mouse heavy-chain apoferritin
Organism:
Fitted atomic model:
Mus musculus
7a4m (1 chains, 698 atoms)

Model evaluation bars:

Model Metric Evaluation bar Average value
7a4m Q-score
0.911
Atom Inclusion
0.752
CCC
0.474
SMOC
0.396

Additional validation information

Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-11638) and model-map (7a4m and EMD-11638). 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:
0.116
256 × 256 × 256
0.533 × 0.533 × 0.533 Å
-0.159
0.521
-0.001
0.026
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 1.30 1.26 1.26 1.21
FSC 0.5 1.45 1.42 1.43 1.35
FSC half-bit 1.32 1.29 1.30 1.23

Map and 1 fitted model

Map with model 7a4m (Cryo-EM structure of mouse heavy-chain apoferritin at 1.22 A)
Primary map with model views
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X

Y projection

Y

Z projection

Z

Map with assembled model views
Title
X projection

X

Y projection

Y

Z projection

Z

Map-model fit plots
Chain scores summary

Depositor mask(s)

Mask with primary map (msk_1)
Title
X projection

X

Y projection

Y

Z projection

Z

EMDB generated mask(s)

FSC mask with raw map
Title
X projection

X

Y projection

Y

Z projection

Z

Symmetry Information
  • Symmetry table (Applied symmetry: O)
    • Symmetry type Symmetry fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees) Peak height
      Symmetry axis #1 C 2 +0.0389, -0.0008195, +0.9992 +180 +0.8494
  • Symmetry element table
    • Symmetry element type Symmetry element fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees)
      Symmetry element #1 E +1 +1, +0, +0 +0
      Symmetry element #2 C +2 +0.0389, -0.0008195, +0.9992 +180
  • Alternative symmetry information
    • Symmetry element type Symmetry element fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees) Peak Height
      Alternative Symmetry #1 C 2 +0.03878, -0.0008171, +0.9992 +180 +0.8557
      Alternative Symmetry #2 C 2 +0.04479, +0.999, -0.002455 +180 +0.6525
      Alternative Symmetry #3 D 2 +0.03878, -0.0008171, +0.9992 +180 +0.8557