Estimating loop length from CryoEM images at medium resolutions

McKnight, Andrew; Si, Dong; Al Nasr, Kamal; Chernikov, Andrey; Chrisochoides, Nikos; He, Jing

doi:10.1186/1472-6807-13-S1-S5

BMC Structural Biology

Table 1 Accuracy of the loop length estimation in the simulated data set.

From: Estimating loop length from CryoEM images at medium resolutions

No	ID	AA	Expected	Measured	Diff	RelErr	DP ∈
1	1ARO	1	7.6	7.4396	0.1604	2.1	1.00
2	1B0B	1	7.6	7.7384	0.1384	1.8	1.25
3	1BGP	1	7.6	7.6755	0.0755	1.0	1.30
4	1BQB	1	7.6	8.0995	0.4995	6.6	2.30
5	1GUX	1	7.6	7.8102	0.2102	2.8	6.00
6	1B43	2	11.4	11.4264	0.0264	0.2	0.45
7	1B89	2	11.4	11.8811	0.4811	4.2	2.55
8	1BD8	2	11.4	11.3578	0.0422	0.4	0.00
9	1BPY	2	11.4	11.4800	0.0800	0.7	2.25
10	1BR1	2	11.4	11.1461	0.2539	2.2	0.00
11	1FJL	3	15.2	15.4724	0.2724	1.8	1.35
12	1FK5	3	15.2	14.9523	0.2477	1.6	0.00
13	1FUR	3	15.2	15.2643	0.0643	0.4	6.00
14	1H0M	3	15.2	15.3601	0.1601	1.1	2.70
15	1DU0	3	15.2	14.9900	0.2100	1.4	0.60
16	1A87	4	19.0	18.8901	0.1099	0.6	0.95
17	1AIH	4	19.0	19.2057	0.2057	1.1	6.00
18	1AJ8	4	19.0	4.1231	14.8769	78.3	0.00
19	1BMT	4	19.0	19.2313	0.2313	1.2	5.55
20	1BOU	4	19.0	18.9609	0.0391	0.2	0.70
21	1D8L	5	22.8	23.1403	0.3403	1.5	0.60
22	1DI1	5	22.8	22.9243	0.1243	0.5	4.25
23	1DLC	5	22.8	22.5618	0.2382	1.0	0.00
24	1DNP	5	22.8	23.1044	0.3044	1.3	1.70
25	1DP7	5	22.8	22.7786	0.0214	0.1	2.10
26	1CQX	6	26.6	26.2583	0.3417	1.3	0.00
27	1CSH	6	26.6	26.9157	0.3157	1.2	1.85
28	1HM6	6	26.6	7.1461	18.8539	26.3	0.00
29	1MW8	6	26.6	26.2419	0.3581	1.3	0.00
30	1O6L	6	26.6	26.6271	0.0271	0.1	6.00
31	1DJX	7	30.4	30.7842	0.3842	1.3	3.85
32	1E5Q	7	30.4	30.5342	0.1342	0.4	4.65
33	1FFV	7	30.4	30.0703	0.3297	1.1	2.50
34	1H99	7	30.4	30.1897	0.2103	0.7	0.00
35	1IRX	7	30.4	30.7213	0.3213	1.1	6.00
36	1O6L	8	34.2	34.6762	0.4762	1.4	6.00
37	1QVR	8	34.2	34.2838	0.0838	0.2	0.60
38	1S0V	8	34.2	34.2505	0.0505	0.1	0.95
39	1TAU	8	34.2	34.3267	0.1267	0.4	0.70
40	1U09	8	34.2	34.1468	0.0532	0.2	2.05
41	1D6M	9	38.0	38.1574	0.1574	0.4	1.00
42	1FUR	9	38.0	38.3249	0.3249	0.9	2.85
43	1H32	9	38.0	38.1491	0.1491	0.4	0.70
44	1QPC	9	38.0	37.9111	0.0889	0.2	0.00
45	1SU8	9	38.0	37.9337	0.0663	0.2	0.65
46	1QRT	10	41.8	41.7369	0.0631	0.2	0.75
47	1R1H	10	41.8	41.3131	0.4869	1.2	0.00
48	1RJB	10	41.8	41.8528	0.0528	0.1	1.00
49	1XO0	10	41.8	41.8814	0.0814	0.2	1.05
50	2B63	10	41.8	41.4589	0.3411	0.8	4.60

ID: PDB ID from which the loop came; AA: the number of amino acids in the loop; Expected = (AA + 1) * 3.8Å; Measured: the estimated length of the loop along the skeleton or its simplification; Diff: Measured - Expected; RelErr: Difference/Expected; DP ∈ is the value that produced the minimum Diff in the estimation.

Back to article page

ISSN: 1472-6807

Contact us

General enquiries: ORSupport@springernature.com