Map Challenge: Resolution Estimation from Half-Maps using FSC Server

Analyis performed by Maya Holmdahl @ PDBe/EBI May/June 2016

Updated July 8, 2016 (emcd154_BetaGal)

Purpose

Standard FSC calculation between submitted half-maps. This gives an idea of how consistent information is as a function of spatial frequency.
For independent half-maps the 0.143 cut-off gives us an indication of the resolution to which we can consider the information reliable.

Method

Masks, when supplied with the submission, were applied to the odd and even map separately using bsoft.
Command: bop -multiply 1,0 <half map> <mask> <output file>
Multiply two images, scaling and shifting the second, according to Scale put to 1 and shift to 0.
FSC calculation was performed using the FSC server: http://pdbe.org/fsc

Results

Results are provided below for each target. For each FSC plot obtained, the resolution at which the correlation crossed 0.5 and 0.143 are recorded below.
Bar charts plot recorded values @ 0.143. Clicking on the "plot" links in the tables below will display the FSC server-generated image.











1. GroEL in silico

plot
submission FSC no mask FSC with mask Reported Resolution
emcd Structure Voxel size
0.5 ( ) 0.143 ( )
0.5 ( ) 0.143 ( ) Submitted Map ( ) Reference EMDB Map (Å)
104 GroEL 1.42 plot
5.8 4.5 plot
- - 4.4 ~4
120 GroEL 1.42 plot 6.4 5 plot 5 4.4 4.3 ~4
132 GroEL 1.42 plot 4.5 4
n/a 4.1 ~4
143 GroEL 1.42 plot 5.6 4.5 plot 4.8 4.1 4.2 ~4
153 GroEL 0.8064 plot 6.8 5.7
n/a 5.7 ~4
158 GroEL 1.42 plot 6 4.7 plot 5.3 4.5 3.9 ~4
165 GroEL 1.4199 plot 6.5 5 plot 4.5 3.9 3.9 ~4
168 GroEL 1.42 plot 146 5.6 plot 5.8 4.6 4.1 ~4
169 GroEL 1.42 plot 5.6 4.6
n/a 4.1 ~4














2. T20S Proteasome

plot
submission FSC no mask FSC with mask Reported Resolution
emcd Structure Voxel size
0.5 () 0.143 ()
0.5 () 0.143 () Submitted Map () Reference EMDB Map ()
103 Proteasome 0.982 plot 3.4 3.1 plot
2.9 2.7 2.8 2.8
107 Proteasome 1.315 plot 3.3 2.9 plot 2.9 2.7 2.7 2.8
108 Proteasome 0.982 plot 3 2.7
n/a 2.7 2.8
130 Proteasome 0.7541 plot 4.4 3.8
n/a 2.7 2.8
131 Proteasome 0.7541 plot 4.4 3.8
n/a 2.7 2.8
141 Proteasome 0.982 plot 3.3 3 plot 3.1 2.7 2.7 2.8
144 Proteasome 1.052 plot 3.7 3.3 plot 3.3 3 3.1 2.8
145 Proteasome 1.052 plot 3.6 3.3 plot 3.3 3 3 2.8
162 Proteasome 0.9818 plot 3.9 3.4 plot 3.1 2.8 2.8 2.8















3. Apo-Ferritin

plot
submission FSC no mask FSC with mask Reported Resolution
emcd Structure Voxel size
0.5 () 0.143 ()
0.5 () 0.143 () Submitted Map () Reference EMDB Map ()
112 Ferritin 1.34 plot
4.1 3.7 plot
3.8 3.5 3.5 4.7
118 Ferritin 1.346 plot 4.2 4 plot 4.1 3.7 3.7 4.7
121 Ferritin 1.346 plot 4.3 3.8
n/a 3.1 4.7
122 Ferritin 1.346 plot 7.6 6.3 plot 3.4 3.1 6.3 4.7
124 Ferritin 1.346 plot 23.1 7.2 plot 6 4.2 4.8 4.7
147 Ferritin 1.34 plot 7.9 7
n/a 6.8 4.7
155 Ferritin 1.34 plot 5 4 plot 5 4 3.9 4.7
166 Ferritin 1.346 plot 4.2 3.8 plot 3.9 3.6 3.6 4.7
















4. TRPV1 Channel

plot
submission FSC no mask FSC with mask Reported Resolution
emcd Structure Voxel size
0.5 () 0.143 ()
0.5 () 0.143 () Submitted Map () Reference EMDB Map ()
101 TRPV 1.2 plot
7.1 4.2 plot
3.8 3.3 3.3 3.3
115 TRPV 1.2156 plot 6.9 4.1 plot 3.6 3.1 3.1 3.3
133 TRPV 0.6078 plot 7.6 3.4 plot 3.9 3.3 4 3.3
135 TRPV 0.6078 plot 7.4 4.3 plot 3.9 3.2 3.8 3.3
146 TRPV 0.6078 plot 7.2 5.2
n/a 4.1 3.3
156 TRPV 1.2156 plot 3.4 3.3
n/a 3.3 3.3
161 TRPV 1.2156 plot 7.6 4.3 plot 3.7 3.2 3.2 3.3
163 TRPV 1.22 plot 7.6 6.2 plot 4.4 4 3.7 3.3












5. 80S Ribosome

plot
submission FSC no mask FSC with mask Reported Resolution
emcd Structure Voxel size
0.5 () 0.143 ()
0.5 () 0.143 () Submitted Map () Reference EMDB Map (A)
111 Ribosome 1.34 plot
6.5 4.2 plot
6.2 4.2 4 3.2
114 Ribosome 1.34 plot 6.6 4.1 plot 3.9 3.3 3.3 3.2
119 Ribosome 1.34 plot 4.8 3.6 plot 4.5 - 3.1 3.2
123 Ribosome 1.34 plot 4.7 3.6 plot 3.5 3 3.1 3.2
125 Ribosome 1.3399 plot 6.7 4.2 plot 3.5 3.2 3.2 3.2
126 Ribosome 1.34 plot 6.6 4.1 plot 3.9 3.2 3.3 3.2
127 Ribosome 1.34 plot 8.3 4.6 plot 4.3 3.5 3.5 3.2
128 Ribosome 1.34 plot 8.9 4.8 plot 4.5 3.6 3.6 3.2
129 Ribosome 1.34 plot 14.6 7.5 plot 6.9 4.3 4.3 3.2
148 Ribosome 1.34 plot 9.2 5.8 plot 4.8 3.8 3.9 3.2
149 Ribosome 1.34 plot 6.5 4 plot 3.9 3.2 3.3 3.2
150 Ribosome 1.34 plot 6.2 3.9 plot 3.8 3.2 3.2 3.2
151 Ribosome 1.34 plot 6.5 4.1 plot 3.8 3.2 3.2 3.2











6. Brome Mosaic Virus

plot
submission FSC no mask FSC with mask Reported Resolution
emcd Structure Voxel size
0.5 () 0.143 ()
0.5 () 0.143 () Submitted Map () Reference EMDB Map (A)
102 BMV 0.99 plot 4 3.7 plot 3.7 3.4 3.5 3.8
110 BMV 0.99 plot
4.6 4.3 plot 4.3 4.1 4 3.8
136 BMV 0.99 plot
5.7 4.4 plot 4.6 4.2 4.2 3.8
137 BMV 0.99 plot
4.5 4.2 plot 4.2 4 4 3.8
140 BMV 0.99 plot
4.1 3.8 plot 3.9 3.6 3.6 3.8
142 BMV 0.99 plot
4.2 3.8 ?
3.9 3.6 3.7 3.8
152 BMV 0.9741 plot
4.5 3.9
n/a 3.9 3.8













7. Beta-Galactosidase

plot
submission FSC no mask FSC with mask Reported Resolution
emcd Structure Voxel size
0.5 () 0.143 ()
0.5 () 0.143 () Submitted Map () Reference EMDB Map ()
106 BetaGal 1.275 plot
3.6 3.2 plot
3.1 2.8 2.8 3.2
113 BetaGal 1.275 plot 7.1 4.2
n/a 3.5 3.2
116 BetaGal 0.64 plot 4.5 4 plot 3.6 3.4 3.4 3.2
134 BetaGal 0.9058 plot 4.6 4
n/a 3.3 3.2
138 BetaGal 0.6375 plot 4.5 3.9 plot 3.7 3.2 3.3 3.2
139 BetaGal 0.6375 plot 4.5 3.8 plot 3.6 3.2 3.3 3.2
*154 BetaGal 0.6375 plot 2.8 1.8 plot 2.1 2.0 3.1 3.2
157 BetaGal 1.02 plot 6 4.1 plot 3.9 3.5 3.4 3.2
159 BetaGal 1.2 plot 3.9 - plot 3.7
-
3.3 3.2
160 BetaGal 0.96 plot 4.1 3.6 plot 3.9 3.5 3.5 3.2
164 BetaGal 1.2 plot 3.9 - plot 3.7
-
3.3 3.2
167 BetaGal 1.2 plot 4.8 4 plot 3.8
3.4
3.3 3.2

*For emcd154, half-set FSC with criterion=0.99 was used to determine the final map resolution