EMDB Validation Analysis : EMD-22516

EMD-22516 › Validation analysis

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SARS-CoV-2 spike in complex with the S2X35 neutralizing antibody Fab fragment

Validation summary

Resolution:
Method:
Map released:
Last modified:
Sample name:
5.0 Å (depositor provided) (FSC 0.143 CUT-OFF)
Single particle reconstruction
2020-10-14
2020-12-02
SARS-CoV-2 spike in complex with the S2X35 neutralizing antibody Fab fragment
Organism:
Homo sapiens, Severe acute respiratory syndrome coronavirus 2

Additional validation information

Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-22516). 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.

Deposited map parameters

Primary map Half map 1 Half map 2
Recommended contour level 0.4 - -
Number of grid points 400 × 400 × 400 400 × 400 × 400 400 × 400 × 400
Voxel size (Å) 1.160 × 1.160 × 1.160 1.160 × 1.160 × 1.160 1.160 × 1.160 × 1.160
Minimum value -1.152 -2.951 -3.002
Maximum value 2.356 2.725 2.695
Average value 0.004 0.001 0.001
Standard deviation 0.045 0.338 0.340
Image not available

Primary map visualisation

Projections

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

Map visualisation analyses

Projection image zero values*
Map Vertical % Horizontal % Overall %
Primary map -0.36 % -1.59 % 86.45 %
Raw map 0.0 % 0.0 % 0.0 %

* measured on z-projection images. Zero(green) values on the image indicative of low signal or masked voxels

Volume graphs

Map resolution (Å) measured by Fourier Shell Correlation (FSC)
EMDB calculated FSC Author FSC
Threshold Unmasked Masked Corrected Author
FSC 0.143 8.18 4.53 4.53 -
FSC 0.5 11.01 6.14 6.21 -
FSC half-bit 8.43 4.59 4.57 -

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: C3)
    • Symmetry type Symmetry fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees) Peak height
      Symmetry axis #1 C 3 -0.003161, -0.007083, +1 +120 +0.7625
  • 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 +3 -0.003161, -0.007083, +1 -120
      Symmetry element #3 C +3 -0.003161, -0.007083, +1 +120