BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97916
1
3
0.97885
1
Reflection
Resolution: 1.5→29.775 Å / Num. obs: 184436 / % possible obs: 89.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.91 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 6.7
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
1.5-1.54
2.1
0.313
2
15624
7554
0.313
50.8
1.54-1.58
2.2
0.246
3.1
19475
8890
0.246
61.1
1.58-1.63
2.3
0.225
3.3
23862
10203
0.225
72
1.63-1.68
2.5
0.197
3.8
28974
11428
0.197
83.1
1.68-1.73
2.9
0.161
4.6
35887
12448
0.161
93.1
1.73-1.79
3.6
0.148
5
46427
13003
0.148
99.8
1.79-1.86
3.7
0.124
5.9
46309
12602
0.124
100
1.86-1.94
3.7
0.104
6.5
44531
12124
0.104
100
1.94-2.02
3.7
0.088
7.8
42654
11595
0.088
100
2.02-2.12
3.7
0.079
8.2
40950
11152
0.079
100
2.12-2.24
3.7
0.074
8.9
39039
10600
0.074
100
2.24-2.37
3.7
0.071
7
36937
10039
0.071
100
2.37-2.54
3.7
0.066
9.2
34765
9469
0.066
100
2.54-2.74
3.7
0.06
10.1
32430
8810
0.06
100
2.74-3
3.7
0.061
9.4
29906
8137
0.061
100
3-3.35
3.6
0.06
9.4
26893
7394
0.06
100
3.35-3.87
3.6
0.05
11.6
23796
6564
0.05
100
3.87-4.74
3.6
0.045
12.3
20125
5577
0.045
100
4.74-6.71
3.5
0.047
11.9
15558
4386
0.047
100
6.71-29.77
3.4
0.051
9.8
8337
2461
0.051
98.1
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.5→29.775 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.007 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.069 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CL, TARTRATE, AND PEG WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.181
9258
5 %
RANDOM
Rwork
0.151
-
-
-
obs
0.153
184358
89.84 %
-
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: 14.04 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.45 Å2
0 Å2
0 Å2
2-
-
0.33 Å2
0 Å2
3-
-
-
0.11 Å2
Refinement step
Cycle: LAST / Resolution: 1.5→29.775 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8214
0
67
1587
9868
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
8824
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
7769
X-RAY DIFFRACTION
r_angle_refined_deg
1.443
1.944
12091
X-RAY DIFFRACTION
r_angle_other_deg
0.833
3
18208
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.549
5
1161
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.335
24.976
422
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.028
15
1453
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.078
15
40
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
1336
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
10027
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1726
X-RAY DIFFRACTION
r_nbd_refined
0.216
0.2
1769
X-RAY DIFFRACTION
r_nbd_other
0.178
0.2
8083
X-RAY DIFFRACTION
r_nbtor_refined
0.178
0.2
4427
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.2
5006
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.154
0.2
1201
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.299
0.2
19
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.275
0.2
79
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.145
0.2
48
X-RAY DIFFRACTION
r_mcbond_it
1.709
3
5522
X-RAY DIFFRACTION
r_mcbond_other
0.43
3
2175
X-RAY DIFFRACTION
r_mcangle_it
2.53
5
8792
X-RAY DIFFRACTION
r_scbond_it
3.803
8
3724
X-RAY DIFFRACTION
r_scangle_it
5.659
11
3242
LS refinement shell
Resolution: 1.5→1.539 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.265
394
-
Rwork
0.2
7145
-
obs
-
7539
50.33 %
+
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