BaculoviralIAPrepeat-containingprotein2 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / hIAP2 / RING finger ...C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / hIAP2 / RING finger protein 48 / TNFR2-TRAF-signaling complex protein 2
Mass: 39277.156 Da / Num. of mol.: 1 Fragment: BIR3-RING, UNP residues 265-618 with a deletion of S363-D372 Mutation: F378Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: API1, BIRC2, IAP2, MIHB, RNF48 / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / References: UniProt: Q13490
Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2010
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9786 Å / Relative weight: 1
Reflection
Redundancy: 4.9 % / Av σ(I) over netI: 23.74 / Number: 164946 / Rmerge(I) obs: 0.081 / Χ2: 1.06 / D res high: 2.2 Å / D res low: 70 Å / Num. obs: 33419 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.74
70
95.6
1
0.056
1.035
5.2
3.76
4.74
98
1
0.067
1.048
5.1
3.29
3.76
98.6
1
0.069
1.083
5.1
2.99
3.29
99
1
0.08
1.099
5
2.77
2.99
99
1
0.097
1.042
5
2.61
2.77
99.4
1
0.117
1.085
4.9
2.48
2.61
99.3
1
0.14
1.087
4.9
2.37
2.48
99.4
1
0.177
1.088
4.8
2.28
2.37
99.5
1
0.216
1.047
4.8
2.2
2.28
99.6
1
0.281
1.018
4.6
Reflection
Resolution: 1.897→50 Å / Num. obs: 27890 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Χ2: 1.044 / Net I/σ(I): 10
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.897-1.97
4.8
0.532
2729
1
1
99.9
1.97-2.05
4.9
0.364
2720
1.034
1
98.6
2.05-2.14
4.9
0.261
2716
1.064
1
99
2.14-2.25
4.9
0.185
2755
1.039
1
99.3
2.25-2.39
4.9
0.145
2765
1.035
1
99.5
2.39-2.58
4.9
0.109
2747
1.068
1
99.7
2.58-2.84
4.9
0.089
2799
1.044
1
99.8
2.84-3.25
4.9
0.069
2813
1.043
1
99.8
3.25-4.09
4.8
0.045
2854
1.023
1
100
4.09-50
4.5
0.035
2992
1.093
1
99.3
-
Phasing
Phasing
Method: SAD
Phasing MAD
D res high: 2.2 Å / D res low: 66.64 Å / FOM : 0.427 / FOM acentric: 0.479 / FOM centric: 0.171 / Reflection: 17676 / Reflection acentric: 14896 / Reflection centric: 2263
Phasing MAD shell
Resolution (Å)
FOM
FOM acentric
FOM centric
Reflection
Reflection acentric
Reflection centric
9.13-12.79
0.432
0.566
0.188
180
116
64
7.48-9.13
0.499
0.629
0.165
211
152
59
6.49-7.48
0.593
0.694
0.269
253
193
60
5.81-6.49
0.549
0.646
0.215
289
224
65
5.31-5.81
0.542
0.638
0.183
301
237
61
4.91-5.31
0.51
0.585
0.183
333
271
60
4.6-4.91
0.43
0.501
0.13
365
296
68
4.34-4.6
0.408
0.468
0.112
376
313
62
4.11-4.34
0.426
0.486
0.13
404
337
64
3.92-4.11
0.433
0.501
0.085
427
358
66
3.76-3.92
0.426
0.481
0.132
443
374
68
3.61-3.76
0.408
0.461
0.111
461
392
66
3.48-3.61
0.456
0.507
0.121
463
402
60
3.36-3.48
0.462
0.516
0.155
498
424
73
3.26-3.36
0.444
0.489
0.128
512
448
63
3.16-3.26
0.459
0.501
0.177
519
453
65
3.07-3.16
0.477
0.527
0.181
545
469
69
2.99-3.07
0.472
0.522
0.143
563
491
66
2.91-2.99
0.479
0.533
0.15
543
470
64
2.84-2.91
0.478
0.527
0.159
589
513
68
2.78-2.84
0.451
0.494
0.171
599
521
67
2.72-2.78
0.458
0.51
0.174
606
520
66
2.66-2.72
0.419
0.469
0.192
625
522
74
2.61-2.66
0.443
0.483
0.175
639
561
64
2.55-2.61
0.43
0.477
0.174
639
547
67
2.51-2.55
0.422
0.466
0.173
644
554
67
2.46-2.51
0.423
0.467
0.186
671
576
66
2.42-2.46
0.392
0.435
0.163
682
586
65
2.38-2.42
0.386
0.422
0.262
662
565
53
2.34-2.38
0.374
0.422
0.168
702
586
71
2.3-2.34
0.367
0.403
0.212
728
619
68
2.27-2.3
0.361
0.397
0.234
689
584
54
2.23-2.27
0.313
0.346
0.166
701
594
66
2.2-2.23
0.307
0.341
0.217
708
578
68
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
PHENIX
1.6.4_486
refinement
PDB_EXTRACT
3.1
dataextraction
Refinement
Method to determine structure: SAD / Resolution: 1.897→32.778 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8313 / SU ML: 0.25 / σ(F): 0 / Phase error: 23.29 / Stereochemistry target values: MLHL
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2328
1344
4.98 %
Random
Rwork
0.1907
-
-
-
obs
0.1928
26966
95.58 %
-
Solvent computation
Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.523 Å2 / ksol: 0.349 e/Å3
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi