Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
AUTHORS STATE THAT THE AGSD LINKER WAS INTRODUCED ON PURPOSE BY PCR TO REPLACE THE LOOP RESIDUES ...AUTHORS STATE THAT THE AGSD LINKER WAS INTRODUCED ON PURPOSE BY PCR TO REPLACE THE LOOP RESIDUES VEEPIPLPEDAPEDAEQEFKKV OF UNP ENTRY P32589 AND WAS FOUND DISORDERED IN COORDINATE DEPOSITED.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 17 % (w/v) polyethyleneglycol-6000, 50 mM KCl, 100 mM HEPES-KOH pH 7.5, vapor diffusion, temperature 277K
Redundancy: 3.6 % / Av σ(I) over netI: 8.8 / Number: 311015 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / D res high: 2.6 Å / D res low: 103.142 Å / Num. obs: 85497 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Rsym value
Redundancy
8.22
80.85
98.5
1
0.03
0.03
3.6
5.81
8.22
99.5
1
0.044
0.044
3.7
4.75
5.81
99.8
1
0.061
0.061
3.8
4.11
4.75
99.9
1
0.044
0.044
3.8
3.68
4.11
100
1
0.045
0.045
3.8
3.36
3.68
100
1
0.063
0.063
3.8
3.11
3.36
100
1
0.103
0.103
3.8
2.91
3.11
100
1
0.161
0.161
3.8
2.74
2.91
99.9
1
0.244
0.244
3.6
2.6
2.74
99
1
0.353
0.353
3.1
Reflection
Resolution: 2.35→103.142 Å / Num. obs: 115684 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.11 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 9.8
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.35-2.48
3.4
0.472
1.6
56550
16664
0.472
99.7
2.48-2.63
3.8
0.311
2.1
59996
15898
0.311
100
2.63-2.81
3.8
0.196
3.9
56392
14925
0.196
100
2.81-3.03
3.8
0.122
6.2
52504
13909
0.122
100
3.03-3.32
3.8
0.074
10
48626
12863
0.074
100
3.32-3.72
3.8
0.044
15.6
43949
11651
0.044
100
3.72-4.29
3.8
0.038
15.7
38808
10323
0.038
100
4.29-5.25
3.8
0.043
13.2
32892
8769
0.043
99.9
5.25-7.43
3.7
0.034
17.1
25414
6834
0.034
99.6
7.43-80.85
3.6
0.022
21.4
13808
3848
0.022
98.3
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Phasing
Phasing
Method: MAD
Phasing dm
FOM centric: 0.6 / Reflection centric: 8156
Phasing dm shell
Resolution (Å)
FOM
FOM acentric
FOM centric
Reflection
Reflection acentric
Reflection centric
6.7-80.767
0.97
0.97
0.94
5199
4295
904
4.2-6.7
0.93
0.94
0.84
15550
14017
1533
3.4-4.2
0.86
0.86
0.77
19443
17961
1482
2.9-3.4
0.68
0.69
0.58
19515
18257
1258
2.5-2.9
0.41
0.42
0.33
34575
32647
1928
2.4-2.5
0.25
0.25
0.2
21356
20305
1051
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Processing
Software
Name
Version
Classification
NB
MOSFLM
datareduction
SCALA
3.2.25
datascaling
SHELX
phasing
RESOLVE
2.08
phasing
REFMAC
refinement
PDB_EXTRACT
3.005
dataextraction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.676 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.262
5797
5 %
RANDOM
Rwork
0.21
-
-
-
obs
0.213
115424
100 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 34.668 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.15 Å2
0 Å2
0 Å2
2-
-
-1.91 Å2
0 Å2
3-
-
-
2.06 Å2
Refinement step
Cycle: LAST / Resolution: 2.35→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
15327
0
70
428
15825
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
15681
X-RAY DIFFRACTION
r_angle_refined_deg
1.43
1.966
21297
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.119
5
2010
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.362
25
694
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.562
15
2584
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.969
15
78
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
2454
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
11849
X-RAY DIFFRACTION
r_nbd_refined
0.203
0.2
6956
X-RAY DIFFRACTION
r_nbtor_refined
0.298
0.2
10631
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.136
0.2
720
X-RAY DIFFRACTION
r_metal_ion_refined
0.052
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.206
0.2
67
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.187
0.2
18
X-RAY DIFFRACTION
r_mcbond_it
0.563
1.5
10282
X-RAY DIFFRACTION
r_mcangle_it
0.903
2
16070
X-RAY DIFFRACTION
r_scbond_it
1.469
3
6034
X-RAY DIFFRACTION
r_scangle_it
2.283
4.5
5227
LS refinement shell
Resolution: 2.35→2.41 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.363
417
-
Rwork
0.284
7870
-
all
-
8287
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.5387
0.0294
0.1846
1.369
-0.3468
1.3458
-0.0808
0.0408
-0.0518
-0.0645
0.1163
0.1612
0.074
-0.0437
-0.0354
-0.2138
-0.004
0.014
-0.2996
-0.0014
-0.1838
88.5399
77.252
182.948
2
3.5934
1.9003
0.6572
4.3469
-0.4112
2.1616
0.2141
-0.5083
-0.6924
0.3026
-0.1325
-0.1511
0.8328
-0.1239
-0.0816
0.1389
-0.009
0.0748
-0.1734
0.0892
0.0667
86.1923
45.3625
198.3048
3
0.3226
0.8681
-0.1443
7.5981
1.6317
0.8401
0.1871
-0.2552
0.1603
0.481
-0.0754
0.28
0.0484
0.1537
-0.1117
-0.1003
-0.014
0.0472
-0.0538
-0.0909
-0.0336
99.4513
105.166
210.0443
4
1.6106
-0.9456
0.0923
2.1683
0.3339
2.5781
-0.0666
0.0442
0.2493
0.014
0.2243
0.0582
-0.4007
-0.2323
-0.1577
-0.1759
0.0447
0.0307
-0.1823
0.133
-0.0254
71.179
106.2813
183.3528
5
3.9714
-0.7966
-2.6502
9.6899
1.2617
4.4512
0.294
0.3282
0.3443
-2.3871
-0.0263
-1.0334
-0.5476
0.3403
-0.2677
0.4445
-0.0154
0.1708
-0.1261
-0.0875
0.1251
103.9829
107.3796
185.9787
6
2.1532
-0.1499
0.4534
1.5831
-0.4059
1.2679
-0.21
0.3418
-0.0999
-0.0686
-0.0027
-0.2775
-0.0381
0.2282
0.2127
-0.1853
-0.0896
0.0116
-0.0904
-0.0096
-0.2012
74.5669
136.6109
119.4957
7
3.2934
-0.2517
-2.2723
1.12
-0.1989
4.2649
0.2016
1.3939
0.5624
-0.7791
-0.0988
-0.2689
-0.3435
-0.2972
-0.1028
0.2629
-0.1913
0.0206
0.8036
0.3261
0.0588
76.2912
155.3741
90.0559
8
0.7683
0.4656
-0.1394
0.727
1.1638
7.4048
0.141
-0.1943
0.2898
0.0027
-0.1259
0.2056
-0.4835
0.0534
-0.0152
-0.0316
-0.012
-0.0361
-0.0827
-0.1135
0.0259
63.0026
160.8291
150.1681
9
2.3977
0.2861
0.9929
2.9499
0.2884
2.1788
-0.0817
-0.2699
-0.2703
0.3798
-0.2183
-0.5352
-0.0301
0.1336
0.3
-0.2006
-0.0702
-0.0966
-0.0575
0.1988
0.0285
91.4976
133.6687
148.6076
10
5.2166
2.6022
0.8679
5.0558
2.9666
10.1736
0.517
-0.4545
-0.5359
0.8743
-0.081
-0.0877
2.7569
-0.6324
-0.4359
0.6085
-0.0835
-0.254
0.0387
-0.0246
-0.1059
59.4296
136.159
149.6244
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 396
2
X-RAY DIFFRACTION
1
A
1001
3
X-RAY DIFFRACTION
1
A
2001
4
X-RAY DIFFRACTION
1
A
2002
5
X-RAY DIFFRACTION
1
A
2003 - 2081
6
X-RAY DIFFRACTION
1
B
383
7
X-RAY DIFFRACTION
1
A
2097 - 2132
8
X-RAY DIFFRACTION
1
B
415 - 417
9
X-RAY DIFFRACTION
2
A
397 - 500
10
X-RAY DIFFRACTION
2
A
525 - 540
11
X-RAY DIFFRACTION
2
A
2082 - 2085
12
X-RAY DIFFRACTION
2
A
2133 - 2143
13
X-RAY DIFFRACTION
3
A
541 - 654
14
X-RAY DIFFRACTION
3
A
2086 - 2094
15
X-RAY DIFFRACTION
3
B
384
16
X-RAY DIFFRACTION
3
A
2144 - 2158
17
X-RAY DIFFRACTION
3
B
418
18
X-RAY DIFFRACTION
4
B
4 - 229
19
X-RAY DIFFRACTION
4
B
308 - 382
20
X-RAY DIFFRACTION
4
A
2095
21
X-RAY DIFFRACTION
4
B
385 - 413
22
X-RAY DIFFRACTION
4
A
2159 - 2161
23
X-RAY DIFFRACTION
4
B
419 - 441
24
X-RAY DIFFRACTION
5
B
230 - 307
25
X-RAY DIFFRACTION
5
A
2096
26
X-RAY DIFFRACTION
5
B
414
27
X-RAY DIFFRACTION
5
B
442 - 445
28
X-RAY DIFFRACTION
6
C
2 - 396
29
X-RAY DIFFRACTION
6
C
1001
30
X-RAY DIFFRACTION
6
C
2001
31
X-RAY DIFFRACTION
6
C
2002 - 2079
32
X-RAY DIFFRACTION
6
D
1064 - 1071
33
X-RAY DIFFRACTION
6
A
2162
34
X-RAY DIFFRACTION
6
C
2095 - 2129
35
X-RAY DIFFRACTION
6
D
1127 - 1158
36
X-RAY DIFFRACTION
7
C
397 - 498
37
X-RAY DIFFRACTION
7
C
526 - 540
38
X-RAY DIFFRACTION
7
C
2080 - 2083
39
X-RAY DIFFRACTION
7
C
2130 - 2131
40
X-RAY DIFFRACTION
8
C
541 - 655
41
X-RAY DIFFRACTION
8
C
2084 - 2093
42
X-RAY DIFFRACTION
8
C
2132 - 2143
43
X-RAY DIFFRACTION
9
D
4 - 229
44
X-RAY DIFFRACTION
9
D
308 - 382
45
X-RAY DIFFRACTION
9
C
2094
46
X-RAY DIFFRACTION
9
D
1096 - 1124
47
X-RAY DIFFRACTION
9
C
2144 - 2146
48
X-RAY DIFFRACTION
9
D
1182 - 1197
49
X-RAY DIFFRACTION
10
D
230 - 307
50
X-RAY DIFFRACTION
10
D
1125 - 1126
51
X-RAY DIFFRACTION
10
C
2147
52
X-RAY DIFFRACTION
10
D
1198 - 1205
+
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