Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 100 mM Tris (pH 8.2), 50 mM MgCl2, 23% (v/v) pentaerythritol propoxylate (17/8 PO/OH), 10 mM AMPNP, 10 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91841 Å / Relative weight: 1
Reflection
Resolution: 3→39.12 Å / Num. obs: 27204 / % possible obs: 99.8 % / Biso Wilson estimate: 74 Å2
Reflection shell
Resolution: 3→3.16 Å / % possible all: 99.1
-
Processing
Software
Name
Version
Classification
MAR345
datacollection
BUSTER
2.10.0
refinement
XDS
datareduction
SCALA
datascaling
Refinement
Method to determine structure: Refined with Refmac, PDB-ID 4A5B Resolution: 3→38.94 Å / Cor.coef. Fo:Fc: 0.8953 / Cor.coef. Fo:Fc free: 0.8676 / Cross valid method: THROUGHOUT / σ(F): 0 Details: AN ADDITIONAL ALTERNATIVE CONFORMATION OF THE ADENINE BASE OF AMPPNP APPEARS POSSIBLE BASED ON THE 3.0 A ELECTRON DENSITY MAPS. THE DENSITY SUGGESTS THAT AMPPNP WITH AN OCCUPANCY OF 0.8 ...Details: AN ADDITIONAL ALTERNATIVE CONFORMATION OF THE ADENINE BASE OF AMPPNP APPEARS POSSIBLE BASED ON THE 3.0 A ELECTRON DENSITY MAPS. THE DENSITY SUGGESTS THAT AMPPNP WITH AN OCCUPANCY OF 0.8 REPRESENTS THE PREDOMINANT BINDING MODE, BUT AN ADDITIONAL ALTERNATIVE BINDING MODE CANNOT BE EXCLUDED ON THE BASIS OF THE LIMITED RESOLUTION OF 3.0 A AND WAS SET TO AN OCCUPANCY OF 0.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2308
1364
5.02 %
RANDOM
Rwork
0.2024
-
-
-
obs
0.2039
27166
99.78 %
-
Displacement parameters
Biso mean: 56.53 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.2143 Å2
0 Å2
0 Å2
2-
-
11.7361 Å2
0 Å2
3-
-
-
-8.5218 Å2
Refine analyze
Luzzati coordinate error obs: 0.449 Å
Refinement step
Cycle: LAST / Resolution: 3→38.94 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9249
0
46
0
9295
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.007
9522
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.96
12917
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
3363
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
252
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1399
HARMONIC
5
X-RAY DIFFRACTION
t_it
9522
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
1
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
1.8
X-RAY DIFFRACTION
t_other_torsion
19.02
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1227
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
10521
SEMIHARMONIC
4
LS refinement shell
Resolution: 3→3.11 Å / Total num. of bins used: 14
Rfactor
Num. reflection
% reflection
Rfree
0.2856
141
5.03 %
Rwork
0.2481
2663
-
all
0.25
2804
-
obs
-
-
99.78 %
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
0.7209
0.7584
-0.9003
0.4466
-0.779
0.416
0.0019
0.0347
-0.0189
0.0087
-0.0117
-0.009
0.0082
-0.0039
0.0097
-0.084
-0.0898
-0.0076
0.124
-0.0455
0.0417
-7.2104
-27.8578
-92.2086
2
0.9654
0.054
-0.1435
1.1827
-0.341
3.3161
-0.0499
-0.0563
-0.2129
0.0301
-0.0148
0.0134
0.1287
-0.0089
0.0648
-0.1
0.0013
0.0235
-0.0526
0.0188
-0.0405
-12.2721
-27.3058
-45.2929
3
0.0141
0.2939
0.5982
0
1.1011
0.0035
-0.0003
-0.0023
0.0164
-0.0139
0.0092
0.0305
-0.0388
-0.0331
-0.0089
-0.0485
0.1436
0.011
0.0238
-0.0566
0.0424
-23.1848
0.9602
-61.5915
4
1.6814
1.2809
-0.3367
2.5665
-0.3918
1.2612
0.0418
-0.0127
0.3924
0.3664
0.1344
0.4924
-0.0863
-0.1804
-0.1762
-0.094
0.1486
0.1475
-0.0573
0.0448
-0.0797
-35.806
-19.101
-31.938
5
0
0.5266
-2.0253
0.4181
-0.0018
1.0068
0.0015
-0.0415
-0.0102
0.0518
-0.0431
0.0183
-0.0281
-0.0272
0.0416
0.2201
0.0217
0.0754
-0.0463
-0.066
-0.0986
-18.7006
-17.6496
-14.2689
6
0.355
-0.4235
1.2805
0.133
0.3306
1.0211
-0.0085
0.0049
0.0072
0.0069
-0.0097
-0.0087
-0.0138
0.0513
0.0182
-0.0055
-0.1362
-0.004
0.0704
-0.0457
-0.0218
28.7254
14.4013
-73.7238
7
2.6517
-0.2161
-0.7921
1.8055
0.2538
1.3404
-0.0546
-0.0323
0.0186
0.0294
0.0688
-0.0318
-0.5344
0.049
-0.0142
0.1198
0.074
0.0192
-0.1275
-0.0264
-0.219
-4.5737
14.6399
-41.5344
8
0.9885
0.0687
-0.9447
0.1427
0.0632
0
-0.0046
-0.0392
0.0092
0.0104
0.0019
-0.0123
0.0304
0.0164
0.0027
-0.0259
0.0072
-0.0111
0.0086
-0.0153
0.0741
15.0728
-13.3297
-43.0293
9
0.7093
-0.2374
-0.178
1.4371
0.3681
2.3214
-0.0204
-0.1418
-0.135
0.4831
0.0764
-0.187
-0.2395
0.2439
-0.0561
0.3032
0.0163
0.0379
-0.1786
0.0102
-0.3006
-0.1712
7.0435
-14.6153
10
0.0678
-0.555
-2.0887
0.7931
0.7903
0.9008
0.0031
-0.0026
-0.0056
0.047
-0.005
-0.0153
-0.0127
-0.0249
0.0019
0.2061
0.0803
0.1465
-0.0666
-0.0784
-0.0594
-24.8601
5.0731
-17.1824
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{A|35 - A|58}
A
35 - 58
2
X-RAY DIFFRACTION
2
{A|59 - A|256 A|586 - A|629}
A
59 - 256
3
X-RAY DIFFRACTION
2
{A|59 - A|256 A|586 - A|629}
A
586 - 629
4
X-RAY DIFFRACTION
3
{A|257 - A|268}
A
257 - 268
5
X-RAY DIFFRACTION
4
{A|269 - A|394 A|425 - A|585}
A
269 - 394
6
X-RAY DIFFRACTION
4
{A|269 - A|394 A|425 - A|585}
A
425 - 585
7
X-RAY DIFFRACTION
5
{A|395 - A|424}
A
395 - 424
8
X-RAY DIFFRACTION
6
{B|37 - B|58}
B
37 - 58
9
X-RAY DIFFRACTION
7
{B|59 - B|256 B|586 - B|629}
B
59 - 256
10
X-RAY DIFFRACTION
7
{B|59 - B|256 B|586 - B|629}
B
586 - 629
11
X-RAY DIFFRACTION
8
{B|257 - B|268}
B
257 - 268
12
X-RAY DIFFRACTION
9
{B|269 - B|394 B|425 - B|585}
B
269 - 394
13
X-RAY DIFFRACTION
9
{B|269 - B|394 B|425 - B|585}
B
425 - 585
14
X-RAY DIFFRACTION
10
{B|395 - B|424}
B
395 - 424
+
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