Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
The gamma phosphate group of the AMPPNP molecule in the active site was disordered, and hence was ...The gamma phosphate group of the AMPPNP molecule in the active site was disordered, and hence was not modelled by the authors
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris-HCl (pH 8), 20% PEG 3350, 200 mM LiSO4.
-
Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9777 Å
Detector
Type: MAR CCD 130 mm / Detector: CCD / Date: Feb 24, 2015
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9777 Å / Relative weight: 1
Reflection
Resolution: 2.28→48.89 Å / Num. obs: 53787 / % possible obs: 97.4 % / Redundancy: 3.7 % / Rsym value: 0.077 / Net I/σ(I): 16.4
Reflection shell
Resolution: 2.28→2.32 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.508 / % possible all: 75.6
-
Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
1.9_1692
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.285→48.493 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.47 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2327
5343
9.93 %
Rwork
0.2064
-
-
obs
0.209
53787
97.34 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.285→48.493 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6190
0
64
253
6507
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
6412
X-RAY DIFFRACTION
f_angle_d
0.63
8739
X-RAY DIFFRACTION
f_dihedral_angle_d
11.59
2175
X-RAY DIFFRACTION
f_chiral_restr
0.029
971
X-RAY DIFFRACTION
f_plane_restr
0.002
1100
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.285-2.3109
0.2762
143
0.2599
1199
X-RAY DIFFRACTION
72
2.3109-2.3381
0.2911
162
0.2749
1346
X-RAY DIFFRACTION
82
2.3381-2.3666
0.3157
147
0.2663
1472
X-RAY DIFFRACTION
90
2.3666-2.3966
0.2774
163
0.2682
1555
X-RAY DIFFRACTION
93
2.3966-2.4281
0.3035
166
0.2708
1557
X-RAY DIFFRACTION
93
2.4281-2.4614
0.2732
197
0.2463
1547
X-RAY DIFFRACTION
96
2.4614-2.4965
0.305
181
0.2469
1647
X-RAY DIFFRACTION
99
2.4965-2.5338
0.2796
188
0.2519
1635
X-RAY DIFFRACTION
99
2.5338-2.5734
0.2734
185
0.2487
1643
X-RAY DIFFRACTION
100
2.5734-2.6156
0.2884
174
0.2438
1653
X-RAY DIFFRACTION
100
2.6156-2.6607
0.2748
162
0.2395
1668
X-RAY DIFFRACTION
100
2.6607-2.7091
0.2457
216
0.2301
1634
X-RAY DIFFRACTION
100
2.7091-2.7612
0.275
181
0.2262
1663
X-RAY DIFFRACTION
100
2.7612-2.8175
0.2548
185
0.2311
1647
X-RAY DIFFRACTION
100
2.8175-2.8788
0.2431
170
0.2327
1652
X-RAY DIFFRACTION
100
2.8788-2.9457
0.2339
178
0.2118
1670
X-RAY DIFFRACTION
100
2.9457-3.0194
0.2712
148
0.2115
1671
X-RAY DIFFRACTION
100
3.0194-3.101
0.2252
195
0.2117
1677
X-RAY DIFFRACTION
100
3.101-3.1922
0.2358
187
0.2149
1640
X-RAY DIFFRACTION
100
3.1922-3.2953
0.2253
176
0.217
1647
X-RAY DIFFRACTION
100
3.2953-3.413
0.2543
185
0.2105
1672
X-RAY DIFFRACTION
100
3.413-3.5496
0.2335
169
0.2068
1656
X-RAY DIFFRACTION
100
3.5496-3.7111
0.2069
198
0.1977
1649
X-RAY DIFFRACTION
100
3.7111-3.9067
0.2118
177
0.1797
1662
X-RAY DIFFRACTION
100
3.9067-4.1513
0.2053
187
0.1696
1646
X-RAY DIFFRACTION
100
4.1513-4.4717
0.1736
190
0.1589
1663
X-RAY DIFFRACTION
100
4.4717-4.9213
0.1682
189
0.1639
1668
X-RAY DIFFRACTION
100
4.9213-5.6325
0.2007
182
0.1882
1652
X-RAY DIFFRACTION
100
5.6325-7.0928
0.2835
178
0.2182
1675
X-RAY DIFFRACTION
100
7.0928-48.5039
0.2451
184
0.209
1678
X-RAY DIFFRACTION
99
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
1.4415
-1.2304
-3.4276
2.0833
2.6353
8.064
-0.0841
-0.1156
0.0558
0.1102
0.1015
0.1066
0.1408
-0.1579
-0.0229
0.219
0.0205
-0.048
0.306
0.0318
0.2623
-32.1501
-0.0018
22.6944
2
1.0048
-1.5071
-0.8324
6.3348
2.5866
1.7361
-0.1234
0.1177
-0.3534
-0.1127
-0.081
0.2643
0.3591
0.0221
0.1432
0.4538
0.0615
0.0198
0.3206
-0.0204
0.3735
-17.2327
-28.1639
0.2034
3
2.7252
0.5711
-2.6559
1.9497
-0.7931
2.6065
-0.1347
0.7185
-0.1335
0.1818
0.2205
0.371
0.0995
-0.8682
-0.0985
0.3232
-0.0577
-0.0793
0.661
0.1005
0.4399
-54.1732
0.7312
-13.1178
4
5.3151
2.4391
-0.9492
3.181
-0.8418
2.6096
0.1698
0.0827
0.0361
-0.0214
0.0672
0.3004
0.0878
-0.3376
-0.2223
0.2635
0.0357
-0.0628
0.2513
0.0369
0.2178
-34.0021
5.3767
-8.2184
5
3.1695
4.5354
1.7514
7.7285
2.2154
2.0284
0.2357
-0.2557
0.1311
0.4921
-0.1795
-0.6165
-0.4185
0.3066
-0.0534
0.5555
-0.2083
0.0177
0.4894
-0.0812
0.6019
-5.927
40.0668
-6.4848
6
2.7338
2.4235
1.267
2.1168
0.8889
0.8757
0.2202
-0.0641
0.6196
0.2192
-0.046
0.121
-0.4539
0.1427
-0.1179
0.6525
-0.1922
0.1388
0.369
-0.0954
0.548
-17.1495
36.394
-10.3671
7
2.635
-0.762
-0.6385
7.474
-0.8488
2.2297
0.2097
0.0192
0.56
-0.3728
0.0924
0.3315
-0.3662
-0.0584
-0.2253
0.3262
-0.039
-0.0159
0.2683
0.0202
0.3155
-30.2519
24.3696
-18.2443
8
4.9826
1.9234
-0.3444
4.2956
-0.5185
1.3262
-0.0238
0.2481
0.489
-0.3319
0.1613
0.6758
-0.0898
-0.1936
-0.1291
0.3719
0.0114
-0.0614
0.3127
0.0934
0.2786
-35.2365
17.6589
-20.2679
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid4through127 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid128through569 )
3
X-RAY DIFFRACTION
3
chain 'B' and (resid4through99 )
4
X-RAY DIFFRACTION
4
chain 'B' and (resid100through158 )
5
X-RAY DIFFRACTION
5
chain 'B' and (resid159through300 )
6
X-RAY DIFFRACTION
6
chain 'B' and (resid301through396 )
7
X-RAY DIFFRACTION
7
chain 'B' and (resid397through510 )
8
X-RAY DIFFRACTION
8
chain 'B' and (resid511through569 )
+
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