EMDB Validation Analysis : EMD-37515

EMD-37515 › Validation analysis

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Cryo-EM structure of inward-open state human norepinephrine transporter NET bound with antidepressant desipramine in KCl condition.

Validation summary

Resolution:
Method:
Map released:
Last modified:
Sample name:
2.75 Å (depositor provided) (FSC 0.143 CUT-OFF)
Single particle reconstruction
2024-07-31
2025-07-02
NET
Organism:
Fitted atomic model:
Homo sapiens
8wgr (1 chains, 2179 atoms)

Additional validation information

Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-37515) and model-map (8wgr and EMD-37515). 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 1.1 - -
Number of grid points 192 × 192 × 192 192 × 192 × 192 192 × 192 × 192
Voxel size (Å) 1.083 × 1.083 × 1.083 1.083 × 1.083 × 1.083 1.083 × 1.083 × 1.083
Minimum value -4.603 -0.595 -0.584
Maximum value 6.247 1.412 1.412
Average value 0.002 0.003 0.002
Standard deviation 0.159 0.063 0.062
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 1.54 % -1.6 % 9.77 %
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 3.36 3.01 3.02 -
FSC 0.5 3.80 3.28 3.28 -
FSC half-bit 3.42 3.05 3.05 -

Map and 1 fitted model

Model-map metrics
Model-map: Residue averaged value
Q-score SMOC CCC Atom inclusion
8wgr 0.576 0.56 0.739 0.765
Model-map: Whole model value
CCvolume CCmask CCpeaks
8wgr 0.754 0.772 0.533
Model-map evaluation bars:
Model Metric Evaluation bar Average value
8wgr Q-score
0.576
Atom Inclusion
0.765
CCC
0.739
SMOC
0.56
Map with model 8wgr (Cryo-EM structure of inward-open state human norepinephrine transporter NET bound with antidepressant desipramine in KCl condition.)
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:

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
No rotational symmetry has been detected in this map.