#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)
-
Assembly
Deposited unit
H: MAB M33 FAB FRAGMENT, heavy chain L: MAB M33 FAB FRAGMENT, light chain C: MAB M33 FAB FRAGMENT, heavy chain D: MAB M33 FAB FRAGMENT, light chain E: MAB M33 FAB FRAGMENT, heavy chain F: MAB M33 FAB FRAGMENT, light chain O: MAB M33 FAB FRAGMENT, heavy chain P: MAB M33 FAB FRAGMENT, light chain hetero molecules
Mass: 23773.506 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody
MABM33FABFRAGMENT, lightchain
Mass: 23621.037 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
Method to determine structure: MOLECULAR REPLACEMENT Starting model: unpublished in house Fab fragment structure Resolution: 2.5→119 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 32.428 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R: 0.966 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27446
3132
5 %
RANDOM
Rwork
0.22547
-
-
-
obs
0.22799
58977
99.91 %
-
all
-
62797
-
-
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: 78.96 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.24 Å2
0 Å2
4.17 Å2
2-
-
-2.72 Å2
-0 Å2
3-
-
-
-0.21 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→119 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13109
0
105
336
13550
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.02
13573
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
12206
X-RAY DIFFRACTION
r_angle_refined_deg
0.994
1.947
18512
X-RAY DIFFRACTION
r_angle_other_deg
0.641
3.002
28231
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.638
5
1690
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.185
24.696
543
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.842
15
2109
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.784
15
38
X-RAY DIFFRACTION
r_chiral_restr
0.058
0.2
2073
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.021
15328
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
3062
X-RAY DIFFRACTION
r_mcbond_it
1.109
4.36
6796
X-RAY DIFFRACTION
r_mcbond_other
1.108
4.359
6795
X-RAY DIFFRACTION
r_mcangle_it
1.929
6.533
8474
X-RAY DIFFRACTION
r_mcangle_other
1.929
6.534
8475
X-RAY DIFFRACTION
r_scbond_it
0.966
4.403
6777
X-RAY DIFFRACTION
r_scbond_other
0.887
4.366
6670
X-RAY DIFFRACTION
r_scangle_other
1.555
6.526
9897
X-RAY DIFFRACTION
r_long_range_B_refined
5.383
33.862
14352
X-RAY DIFFRACTION
r_long_range_B_other
5.342
33.7
14278
LS refinement shell
Resolution: 2.5→2.565 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.451
234
-
Rwork
0.392
4353
-
obs
-
-
99.8 %
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
0.7363
-0.2273
0.069
0.3946
-0.8653
2.3198
-0.0967
0.0221
-0.0441
0.1425
0.0262
-0.0406
-0.1676
-0.2656
0.0705
0.5297
0.0845
-0.2944
0.4946
-0.0944
0.1808
29.1592
-33.5277
55.3877
2
1.2669
-0.0728
0.6366
0.7522
-0.8635
2.3811
-0.0108
-0.0121
-0.1017
-0.0692
-0.0587
0.0796
0.2286
-0.3487
0.0695
0.5605
0.0652
-0.2341
0.5826
-0.0862
0.1781
22.4354
-50.2362
55.6086
3
1.1377
-0.2187
-0.1537
2.01
-0.3723
1.8892
0.0946
-0.0085
0.2636
-0.1439
-0.0194
-0.1704
-0.0173
0.3378
-0.0752
0.3838
-0.0257
-0.1493
0.4644
-0.0554
0.1653
16.0839
-12.1785
-7.2661
4
1.947
0.4974
-0.0183
1.8021
-0.7663
2.5646
-0.0377
0.4704
0.1128
-0.3034
-0.0137
0.2951
-0.0368
-0.374
0.0513
0.5525
0.1295
-0.2848
0.5946
-0.0566
0.1641
0.0159
-15.9707
-15.4827
5
1.1902
-0.1244
0.4197
0.9874
0.3534
2.1675
0.1017
-0.0484
0.1808
-0.2834
-0.1511
-0.1346
-0.0843
-0.1994
0.0494
0.2365
0.0046
-0.0785
0.3291
-0.0026
0.1525
-43.2369
-38.1434
0.4716
6
1.6398
-0.2716
0.9846
1.8126
2.0016
4.3593
0.0656
0.0904
0.1867
0.0503
-0.0775
0.0814
0.5375
-0.0408
0.012
0.1924
-0.0495
-0.0756
0.2957
-0.0926
0.1229
-40.1487
-55.9993
1.3046
7
1.7153
1.5191
-0.0351
2.6327
-0.1035
0.5134
0.2117
-0.353
0.0821
0.5118
-0.1939
0.1914
-0.122
-0.0301
-0.0177
0.5133
0.0796
-0.113
0.5039
-0.021
0.0773
-9.351
-21.2043
43.2018
8
2.2693
1.4081
-1.3201
1.7025
-1.0181
1.9062
0.0988
0.0225
0.164
0.1872
-0.0224
0.3877
-0.2178
-0.2774
-0.0764
0.2664
0.0733
-0.1409
0.2593
-0.0569
0.2615
-25.0422
-15.604
37.0236
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
H
1 - 220
2
X-RAY DIFFRACTION
2
L
1 - 213
3
X-RAY DIFFRACTION
3
C
2 - 220
4
X-RAY DIFFRACTION
4
D
1 - 211
5
X-RAY DIFFRACTION
5
E
1 - 219
6
X-RAY DIFFRACTION
6
F
1 - 213
7
X-RAY DIFFRACTION
7
O
1 - 220
8
X-RAY DIFFRACTION
8
P
1 - 210
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
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