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 monochromator (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
0.979197
1
Reflection
Resolution: 1.95→29.488 Å / Num. obs: 22592 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.19 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.6
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
1.95-2
3.5
0.648
1.2
5816
1645
0.648
99.7
2-2.06
3.5
0.507
1.5
5752
1621
0.507
99.7
2.06-2.12
3.5
0.396
1.9
5582
1574
0.396
99.8
2.12-2.18
3.5
0.32
2.4
5381
1518
0.32
99.4
2.18-2.25
3.6
0.293
2.4
5195
1459
0.293
99.4
2.25-2.33
3.5
0.258
2.9
5025
1422
0.258
99.5
2.33-2.42
3.5
0.216
3.5
4923
1407
0.216
99.6
2.42-2.52
3.5
0.197
3.8
4668
1325
0.197
99.7
2.52-2.63
3.5
0.155
4.9
4448
1276
0.155
99.7
2.63-2.76
3.5
0.124
6
4240
1222
0.124
99.6
2.76-2.91
3.5
0.101
7.4
4085
1182
0.101
99.6
2.91-3.08
3.4
0.079
9
3815
1111
0.079
99.3
3.08-3.3
3.4
0.061
11.5
3604
1049
0.061
98.9
3.3-3.56
3.3
0.049
13.4
3236
975
0.049
99.2
3.56-3.9
3.3
0.043
15.1
2975
910
0.043
98.4
3.9-4.36
3.1
0.038
14.5
2460
789
0.038
94.9
4.36-5.03
3.4
0.049
11.4
2388
701
0.049
96.4
5.03-6.17
3.5
0.046
12.7
2220
641
0.046
99.5
6.17-8.72
3.4
0.043
14.7
1706
500
0.043
98.8
8.72-29.49
3
0.049
10.2
802
265
0.049
89.3
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.95→29.488 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.387 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.165 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RESIDUES A115-128 AND B119-127 ARE DISORDERED AND WERE NOT MODELED. 5. FAD MODELED BASED ON PROPOSED FUNCTION AND DENSITY. 6. ETHYLENE GLYCOL AND CHLORIDE MODELED BASED ON CRYSTALLIAZTION CONDITIONS. 7. THERE IS UNMODELED DENSITY NEAR A135, B42 AND B135.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.243
1162
5.2 %
RANDOM
Rwork
0.18
-
-
-
all
0.183
-
-
-
obs
0.183
22557
98.79 %
-
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: 27.524 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.67 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.68 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→29.488 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2164
0
111
178
2453
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.021
2369
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2089
X-RAY DIFFRACTION
r_angle_refined_deg
1.645
1.993
3240
X-RAY DIFFRACTION
r_angle_other_deg
0.834
3
4831
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.843
5
277
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.224
22.353
102
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.27
15
365
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.817
15
19
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
340
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2555
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
488
X-RAY DIFFRACTION
r_nbd_refined
0.185
0.2
445
X-RAY DIFFRACTION
r_nbd_other
0.195
0.2
2142
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.2
1126
X-RAY DIFFRACTION
r_nbtor_other
0.086
0.2
1391
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.163
0.2
135
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.233
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.178
0.2
68
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.162
0.2
16
X-RAY DIFFRACTION
r_mcbond_it
1.018
1.5
1391
X-RAY DIFFRACTION
r_mcbond_other
0.255
1.5
561
X-RAY DIFFRACTION
r_mcangle_it
1.707
2
2195
X-RAY DIFFRACTION
r_scbond_it
2.305
3
1215
X-RAY DIFFRACTION
r_scangle_it
3.621
4.5
1041
LS refinement shell
Resolution: 1.95→2.001 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.333
107
-
Rwork
0.226
1537
-
obs
-
1644
99.52 %
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
0.8431
-0.6252
-1.1759
0.7562
1.2072
3.2042
-0.1255
0.048
-0.0125
0.0226
0.0615
0.0055
0.3526
0.1385
0.064
-0.0607
0.002
0.007
-0.1091
0.005
-0.0827
37.742
36.97
16.14
2
1.4917
-0.6693
-1.2244
1.3818
0.9515
3.3368
0.1161
0.1178
0.0942
-0.117
0.008
0.0629
-0.2776
-0.0878
-0.1241
-0.0979
-0.0074
-0.004
-0.1018
0.0073
-0.0916
29.278
52.837
27.627
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
0 - 148
1 - 149
2
2
B
B
1 - 147
2 - 148
+
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