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Fitting EM maps into X-ray Data
Alexei VaginYork Structural Biology LaboratoryUniversity of
York
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EM X-ray ( P2 )--> MR -->H2OH2O
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Molecular ReplacementCellModel1. Rotation function2.Translation
function
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Can we find solution?Weight of low resolution growsLow high
Model Similarity0 .1 0.2 0.3 0.4 0.5 Weight of high resolution
growsLow high Model size0.5 0.4 0.3 0.2 0.1Very likelyVery
unlikelyEM model
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Information in X-ray and EMmust overlapsResmin X-rayResmax
EM
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Example 1 Groel-ATP7-Groes Map: EMD-1180Fitted atomic model: PDB
2c7c
X-ray: PDB 1sx4 ( 40 - 3 A )
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EM map as model
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EM map (sfcheck) from grid
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EM map (sfcheck) 7A
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Information in X-ray and EMmust overlapsResmin X-ray (40A)Resmax
EM (7A)
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Ph =Phxray - Phem MR solution (EM model) Ph =Phxray - Phmodel MR
solution (fitted atomic model)
50o90oRes: 11.1 9.1 7.7 6.7 5.9 5.3 4.8 4.3 4.0 APh
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Map ( Fobs Phem ) 6
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What we can do with these phases1. Help to find HA positions in
the derivative2. Extend phases by averaging electron density3. Try
to fit some fragments ( helix )
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EM map (4A) Modified mapAveraging and Solvent flattening
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Map (FobsPhem) 4 Modified map
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Ph =Phxray - Phem MR solution (EM model) Ph =Phxray - Phmodel MR
solution (fitted atomic model)Ph =Phxray - Phaver MR solution
(after DM) 50o90oRes: 11.1 9.1 7.7 6.7 5.9 5.3 4.8 4.3 4.0 APh
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Free atom model
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Ph =Phxray - Phem MR solution (EM model) Ph =Phxray - Phmodel MR
solution (fitted atomic model) Ph =Phxray - Phmodel_ref MR solution
(refined atomic model) Ph =Phxray - Phfree MR solution (free atom
model after DM) 50o90oRes: 9.4 7.4 6.1 5.2 4.5 4.0 3.6 3.3 3.0
APh
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Map (FobsPhem) 3 Map (FobsPhfree) 3 (Free atom model after
DM)
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Map (FobsPhfree) 3 (Free atom model after DM)
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Map (FobsPhfree) 3 (Free atom model after DM)
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Example 2 X-ray structure of GP6 protein of phage SPP1 ( 3.4 A
)Fred Antson at al.University of York
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EM map as model
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EM map (sfcheck 1)from grid
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EM map (sfcheck 2)8A
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Information in X-ray and EMmust overlapsResmin X-ray (40A)Resmax
EM (8A)
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Ph =Phxray - Phem MR solution (EM model) 50o90oRes: 10.3 8.3 6.9
6.0 5.2 4.7 4.2 3.8 3.5 APh
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Map ( Fobs Phem ) 7
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What we can do with these phases1. Help to find HA positions in
the derivative2. Extend phases by averaging electron density3. Try
to fit some fragments ( helix )
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Ph =Phxray - Phem MR solution (EM model) Ph =Phxray - Phaver MR
solution (after DM) 50o90oRes: 10.3 8.3 6.9 6.0 5.2 4.7 4.2 3.8 3.5
APh
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Free atom modelmodel was used only to compute initial phases
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Ph =Phxray - Phem MR solution (EM model) Ph =Phxray - Phaver MR
solution (after DM) Ph =Phxray - Phfree MR solution (free atom
model after DM) 50o90oRes: 10.3 8.3 6.9 6.0 5.2 4.7 4.2 3.8 3.5
APh
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Final map 3.5 A
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Final map 3.5 A
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Map ( Fobs Phem ) Final map
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What we can do with these phases1. Help to find HA positions in
the derivative2. Extend phases by averaging electron density3. Try
to fit some fragments ( helix )
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Fitting 17 x 13 helixes into final map by SAPTF
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Final map 3.5 A and helixes
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X-ray model and helixes
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Model: helix_17x13.pdb 1.Refinement2.Compute map for refined
model3.Combine final map and map from modelFinal map Combine
map
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Ph =Phxray - Phem MR solution (EM model) Ph =Phxray - Phaver MR
solution (after DM) Ph =Phxray - Phfree MR solution (free atom
model after DM) Ph =Phxray - Phcomb combine map 50o90oRes: 10.3 8.3
6.9 6.0 5.2 4.7 4.2 3.8 3.5 APh
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The endhttp://www.ysbl.york.ac.uk/~alexei/
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SOLUTION_CHECK: Are two solutions identical?
Alexei VaginYork Structural Biology LaboratoryUniversity of
York
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It is trivial.
Xtest[Torigin][Tsymm_op]YtestXtargetAlignment,
FittingOrientation and position differences
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The end
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