EMD-9216 Validation analysis

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Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome

Validation summary

Resolution:

Method:

Map released:

Last modified:

Sample name:

3.0 Å (depositor provided) (FSC 0.143 CUT-OFF)

Single particle reconstruction

2018-12-05

2025-05-14

Human 26S proteasome

Organism:

Fitted atomic model:

Homo sapiens

6msb (48 chains, 102919 atoms)

Additional validation information

Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-9216) and model-map (6msb and EMD-9216). 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	0.0035	-	-
Number of grid points	600 × 600 × 600	-	-
Voxel size (Å)	0.685 × 0.685 × 0.685	-	-
Minimum value	-0.006	-	-
Maximum value	0.023	-	-
Average value	0.000	-	-
Standard deviation	0.001	-	-

Primary map visualisation

Projections

Volume graphs

Download data (depositor): Depositor Half Map 1 Depositor Half Map 2

Download data (EMDB derived): EMDB Mask Learn more EMDB Raw Map Learn more

Map and 1 fitted model

Model-map metrics

Model-map: Residue averaged value

	Q-score	SMOC	CCC	Atom inclusion
6msb	0.389	0.725	0.85	0.886

Model-map: Whole model value

	CCvolume	CCmask	CCpeaks
6msb	0.827	0.839	0.750

Model-map evaluation bars:

Model	Metric	Average value
6msb	Q-score	0.389
	Atom Inclusion	0.886
	CCC	0.85
	SMOC	0.725

Map with model 6msb (Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome)

Primary map with model views

Title

Model-map fit plots

Chain scores summary

Plot

Chain Number of atoms Atom inclusion Q-score

A 3063 0.904 0.433

B 2999 0.908 0.427

C 2832 0.913 0.439

D 3012 0.902 0.428

E 2831 0.903 0.425

F 2840 0.898 0.434

G 1796 0.946 0.492

H 1678 0.955 0.499

I 1874 0.946 0.47

J 1673 0.956 0.471

K 1706 0.947 0.485

L 1807 0.953 0.493

M 1817 0.941 0.478

N 1398 0.964 0.517

O 1614 0.978 0.513

P 1562 0.967 0.518

Q 1535 0.967 0.508

R 1498 0.971 0.514

S 1605 0.96 0.511

T 1623 0.962 0.522

U 6239 0.862 0.27

V 3903 0.786 0.231

W 3630 0.796 0.247

X 2956 0.847 0.323

Y 3031 0.894 0.321

Z 2249 0.851 0.309

a 2949 0.851 0.248

b 1441 0.801 0.155

c 2232 0.869 0.365

d 2076 0.813 0.218

e 330 0.754 0.162

f 6754 0.719 0.161

g 1796 0.952 0.491

h 1678 0.946 0.497

i 1874 0.908 0.443

j 1666 0.931 0.428

k 1706 0.942 0.473

l 1807 0.956 0.486

m 1817 0.934 0.474

n 1398 0.97 0.525

o 1614 0.973 0.519

p 1562 0.971 0.523

q 1535 0.972 0.516

r 1498 0.981 0.529

s 1608 0.968 0.515

t 1623 0.969 0.525

u 592 0.02 -0.016

w 592 0.108 0.012

All 102919 0.886 0.389

Chain	Number of atoms	Atom inclusion	Q-score
A	3063	0.904	0.433
B	2999	0.908	0.427
C	2832	0.913	0.439
D	3012	0.902	0.428
E	2831	0.903	0.425
F	2840	0.898	0.434
G	1796	0.946	0.492
H	1678	0.955	0.499
I	1874	0.946	0.47
J	1673	0.956	0.471
K	1706	0.947	0.485
L	1807	0.953	0.493
M	1817	0.941	0.478
N	1398	0.964	0.517
O	1614	0.978	0.513
P	1562	0.967	0.518
Q	1535	0.967	0.508
R	1498	0.971	0.514
S	1605	0.96	0.511
T	1623	0.962	0.522
U	6239	0.862	0.27
V	3903	0.786	0.231
W	3630	0.796	0.247
X	2956	0.847	0.323
Y	3031	0.894	0.321
Z	2249	0.851	0.309
a	2949	0.851	0.248
b	1441	0.801	0.155
c	2232	0.869	0.365
d	2076	0.813	0.218
e	330	0.754	0.162
f	6754	0.719	0.161
g	1796	0.952	0.491
h	1678	0.946	0.497
i	1874	0.908	0.443
j	1666	0.931	0.428
k	1706	0.942	0.473
l	1807	0.956	0.486
m	1817	0.934	0.474
n	1398	0.97	0.525
o	1614	0.973	0.519
p	1562	0.971	0.523
q	1535	0.972	0.516
r	1498	0.981	0.529
s	1608	0.968	0.515
t	1623	0.969	0.525
u	592	0.02	-0.016
w	592	0.108	0.012
All	102919	0.886	0.389

Strudel Information

Chain:

Score range:

Symmetry Information

Symmetry table (Applied symmetry: C1)

	Symmetry type	Symmetry fold	Directional vector of symmetry axis X, Y, Z	Angle (degrees)	Peak height
Symmetry axis #1	C	13	+0.9808, -0.1211, -0.1523	+27.69	+0.06824
Symmetry axis #2	C	2	+0.1251, +0.9063, -0.4037	+180	+0.05172

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	4	+0.9816, -0.1233, -0.1456	-90
Symmetry element #3	C	4	+0.9816, -0.1233, -0.1456	+90
Symmetry element #4	C	4	+0.9816, -0.1233, -0.1456	+180
Symmetry element #5	C	2	+0.1251, +0.9063, -0.4037	+180

Alternative symmetry information

	Symmetry element type	Symmetry element fold	Directional vector of symmetry axis X, Y, Z	Angle (degrees)	Peak Height
Alternative Symmetry #1	C	3	+0.9824, -0.1357, -0.1284	+120	+0.0951
Alternative Symmetry #2	C	13	+0.9808, -0.1211, -0.1523	+27.69	+0.06824
Alternative Symmetry #3	C	2	+0.1006, +0.7408, -0.6642	+180	+0.05377
Alternative Symmetry #4	C	2	+0.1251, +0.9063, -0.4037	+180	+0.05172
Alternative Symmetry #5	C	4	+0.9817, -0.1218, -0.1462	+90	+0.05159
Alternative Symmetry #6	C	2	+0.1817, +0.9822, -0.02667	+180	+0.04543
Alternative Symmetry #7	C	2	-0.04202, -0.5492, +0.8346	+180	+0.04436
Alternative Symmetry #8	D	3	+0.9824, -0.1357, -0.1284	+120	+0.0951
Alternative Symmetry #9	D	3	+0.9824, -0.1357, -0.1284	+120	+0.0951
Alternative Symmetry #10	D	3	+0.9824, -0.1357, -0.1284	+120	+0.0951
Alternative Symmetry #11	D	3	+0.9824, -0.1357, -0.1284	+120	+0.0951
Alternative Symmetry #12	D	13	+0.9808, -0.1211, -0.1523	+27.69	+0.06824
Alternative Symmetry #13	D	13	+0.9808, -0.1211, -0.1523	+27.69	+0.06824
Alternative Symmetry #14	D	2	+0.1251, +0.9063, -0.4037	+180	+0.05172
Alternative Symmetry #15	D	4	+0.9817, -0.1218, -0.1462	+90	+0.05159
Alternative Symmetry #16	D	4	+0.9817, -0.1218, -0.1462	+90	+0.05159

Navigation link

EMDB Validation Analysis : EMD-9216