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.
Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Sequence details
REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: NANODROP, 0.2M NaCl, 20.0% PEG 8000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 2.2→15.895 Å / Num. obs: 31068 / % possible obs: 95.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 37.26 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 7.9
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
2.2-2.32
1.9
0.417
1.7
8679
4574
0.417
97.1
2.32-2.46
1.9
0.272
2.8
8233
4354
0.272
97
2.46-2.63
1.9
0.191
3.9
7727
4078
0.191
96.9
2.63-2.84
1.9
0.128
5.9
7214
3829
0.128
97.3
2.84-3.11
1.9
0.082
8.4
6596
3503
0.082
96.9
3.11-3.48
1.9
0.056
11.4
5922
3135
0.056
96
3.48-4.02
1.9
0.045
13.6
5178
2727
0.045
94.6
4.02-4.92
1.8
0.035
18.2
4129
2250
0.035
91.5
4.92-6.96
2
0.04
15.3
3561
1752
0.04
93
6.96-15.895
2.1
0.035
12.6
1826
872
0.035
82.5
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.3.0040
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
ADSC
Quantum
datacollection
MOSFLM
datareduction
SHELXD
phasing
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.2→15.895 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.317 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.248 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. RESIDUES 0-1 IN CHAIN A, 0-1, 78-84 IN CHAIN B, 0-1 IN CHAIN C, AND 0-1, 78-85 IN CHAIN D ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. GOL AND PO4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 6. R-FACTORS ARE SLIGHTLY HIGH, ESPECIALLY NEAR 5.5 A RESOLUTION SHELL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.275
1581
5.1 %
RANDOM
Rwork
0.223
-
-
-
obs
0.225
31066
95.45 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 39.499 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.51 Å2
0 Å2
0.16 Å2
2-
-
-0.35 Å2
0 Å2
3-
-
-
-0.04 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→15.895 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4333
0
34
224
4591
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
4462
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
2979
X-RAY DIFFRACTION
r_angle_refined_deg
1.411
1.993
6056
X-RAY DIFFRACTION
r_angle_other_deg
1.275
3
7357
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.131
5
551
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
28.684
25.248
202
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.745
15
846
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.545
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.081
0.2
739
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
4813
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
779
X-RAY DIFFRACTION
r_nbd_refined
0.15
0.2
957
X-RAY DIFFRACTION
r_nbd_other
0.111
0.2
2741
X-RAY DIFFRACTION
r_nbtor_refined
0.133
0.2
2090
X-RAY DIFFRACTION
r_nbtor_other
0.071
0.2
2099
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.084
0.2
170
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.055
0.2
29
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.13
0.2
61
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.057
0.2
12
X-RAY DIFFRACTION
r_mcbond_it
0.977
3
3422
X-RAY DIFFRACTION
r_mcbond_other
0.199
3
1086
X-RAY DIFFRACTION
r_mcangle_it
1.288
5
4456
X-RAY DIFFRACTION
r_scbond_it
3.07
8
1823
X-RAY DIFFRACTION
r_scangle_it
4.372
11
1594
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
749
MEDIUMPOSITIONAL
0.31
0.5
2
B
749
MEDIUMPOSITIONAL
0.26
0.5
3
C
749
MEDIUMPOSITIONAL
0.32
0.5
4
D
749
MEDIUMPOSITIONAL
0.24
0.5
1
A
801
LOOSEPOSITIONAL
0.62
5
2
B
801
LOOSEPOSITIONAL
0.57
5
3
C
801
LOOSEPOSITIONAL
0.61
5
4
D
801
LOOSEPOSITIONAL
0.59
5
1
A
749
MEDIUMTHERMAL
0.36
2
2
B
749
MEDIUMTHERMAL
0.25
2
3
C
749
MEDIUMTHERMAL
0.38
2
4
D
749
MEDIUMTHERMAL
0.35
2
1
A
801
LOOSETHERMAL
0.44
10
2
B
801
LOOSETHERMAL
0.33
10
3
C
801
LOOSETHERMAL
0.44
10
4
D
801
LOOSETHERMAL
0.42
10
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.37
143
-
Rwork
0.302
2146
-
all
-
2289
-
obs
-
-
96.87 %
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
2.109
0.5058
-0.1459
2.7553
-1.1174
1.3406
0.0469
0.0048
0.2173
0.1177
0.0615
0.1718
-0.0537
-0.0395
-0.1084
-0.1794
0.0065
0.018
-0.0384
-0.0247
-0.0988
-13.309
19.893
-24.89
2
2.2899
1.4337
0.4146
2.9376
0.9417
3.5014
-0.3997
0.6635
0.3223
-0.5822
0.4645
0.2391
-0.2537
0.1126
-0.0648
0.0129
-0.145
-0.0558
0.1556
0.1407
0.0796
-14.977
31.787
-46.597
3
0.5672
-0.045
-1.0502
0.8424
0.9032
4.2184
-0.019
-0.0757
0.0282
-0.0982
-0.0418
0.0659
-0.0649
0.4552
0.0607
-0.1186
0.0136
-0.0563
0.0966
0.0157
-0.083
18.122
10.005
-55.562
4
3.635
0.2232
1.9143
1.1637
-0.2061
2.0948
0.1823
-0.2707
-0.4936
0.0447
-0.0302
-0.0676
0.3396
-0.2064
-0.1521
-0.1484
-0.0189
0.0246
-0.0131
-0.0044
0.0523
13.376
4.938
-31.988
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
2 - 141
3 - 142
2
X-RAY DIFFRACTION
2
B
B
2 - 77
3 - 78
3
X-RAY DIFFRACTION
2
B
B
85 - 141
86 - 142
4
X-RAY DIFFRACTION
3
C
C
2 - 141
3 - 142
5
X-RAY DIFFRACTION
4
D
D
2 - 77
3 - 78
6
X-RAY DIFFRACTION
4
D
D
86 - 141
87 - 142
+
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