EMDB Validation Analysis : EMD-30849

EMD-30849 › Validation analysis

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Structure of a human NHE1-CHP1 complex under pH 7.5, bound by cariporide

Validation summary

Resolution:
Method:
Map released:
Last modified:
Sample name:
3.5 Å (depositor provided) (FSC 0.143 CUT-OFF)
Single particle reconstruction
2021-06-23
2024-03-27
Human NHE1-CHP1 complex under pH 7.5, bound by cariporide
Organism:
Fitted atomic model:
Homo sapiens
7dsx (4 chains, 10956 atoms)

Additional validation information

Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-30849) and model-map (7dsx and EMD-30849). 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 256 × 256 × 256 - -
Voxel size (Å) 1.040 × 1.040 × 1.040 - -
Minimum value -1.872 - -
Maximum value 2.923 - -
Average value 0.001 - -
Standard deviation 0.087 - -
Image not available

Primary map visualisation

Projections

Volume graphs

Provided FSC(Å)
FSC 0.143 3.49
FSC 0.5 3.79
FSC half-bit -

Map and 1 fitted model

Model-map metrics
Model-map: Residue averaged value
Q-score SMOC CCC Atom inclusion
7dsx 0.456 0.68 0.782 0.727
Model-map: Whole model value
CCvolume CCmask CCpeaks
7dsx 0.730 0.765 0.568
Model-map evaluation bars:
Model Metric Evaluation bar Average value
7dsx Q-score
0.456
Atom Inclusion
0.727
CCC
0.782
SMOC
0.68
Map with model 7dsx (Structure of a human NHE1-CHP1 complex under pH 7.5, bound by cariporide)
Primary map with model views
Title
X projection

X

Y projection

Y

Z projection

Z

Model-map fit plots
Threshold comparison:
Chain scores summary
Strudel Information
Chain:
Score range:
Symmetry Information
  • Symmetry table
    • Symmetry type Symmetry fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees) Peak height
      Symmetry axis #1 C 2 +0.00283, +0.01073, +0.9999 +180 +0.955
  • 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 +0.00283, +0.01073, +0.9999 +180