Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9792 Å / Relative weight: 1
Reflection
Resolution: 3.3→17 Å / Num. obs: 14953 / % possible obs: 98.57 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 82.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.6
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
3.3-3.35
0.478
4.3
4367
639
97.3
3.35-3.4
0.411
5
4341
620
98.9
3.4-3.5
0.353
5.6
7888
1128
99.2
3.5-3.75
0.262
7.6
16213
2320
99.2
3.75-4
0.147
12.6
12465
1787
99.1
4-6
0.066
24.1
40989
5950
98.7
6-8
0.044
32.5
9977
1495
97.8
8-10
0.03
39.9
3275
542
96.6
10-12
0.021
59
1554
246
95.7
12-14
0.023
56.5
775
130
95.6
14-16
0.021
56.9
402
71
95.9
16
0.019
54
140
25
13.8
-
Phasing
Phasing
Method: MIRAS
-
Processing
Software
Name
Version
Classification
NB
XSCALE
dataprocessing
SHARP
phasing
PHENIX
refinement
PDB_EXTRACT
3
dataextraction
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: MIRAS / Resolution: 3.3→16.985 Å / FOM work R set: 0.794 / SU ML: 0.46 / Phase error: 26.76 / Stereochemistry target values: ML / Details: This structure was refined using TLS in PHENIX.
Rfactor
Num. reflection
% reflection
Rfree
0.267
757
5.06 %
Rwork
0.22
-
-
obs
0.222
14953
98.57 %
Solvent computation
Shrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.059 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Biso max: 219.59 Å2 / Biso min: 46.99 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-9.466 Å2
-0 Å2
0 Å2
2-
-
-9.466 Å2
-0 Å2
3-
-
-
18.932 Å2
Refinement step
Cycle: LAST / Resolution: 3.3→16.985 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4412
0
0
0
4412
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Weight
X-RAY DIFFRACTION
f_angle_d
0.944
6108
1
X-RAY DIFFRACTION
f_bond_d
0.006
4506
1
X-RAY DIFFRACTION
f_chiral_restr
0.063
688
1
X-RAY DIFFRACTION
f_dihedral_angle_d
20.254
1659
1
X-RAY DIFFRACTION
f_plane_restr
0.004
791
1
X-RAY DIFFRACTION
f_nbd_refined
4.13
1
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.273 / Total num. of bins used: 5
Resolution (Å)
Num. reflection Rfree
Num. reflection Rwork
% reflection obs (%)
3.3002-3.5529
150
2774
98.78
3.5529-3.9065
155
2795
99.23
3.9065-4.4628
131
2848
99.17
4.4628-5.5892
159
2838
98.49
5.589-16.9854
162
2941
97.27
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
5.3788
0.9633
-2.1458
3.0831
0.6345
2.943
0.0744
0.1555
-1.1965
0.1582
-0.3137
-0.288
0.4884
0.4111
0.0007
0.7434
0.0946
0.0705
0.8763
-0.0385
0.5338
27.6759
1.8796
16.0823
2
3.6431
2.7595
-2.7708
4.6185
-1.5344
3.5706
0.0717
0.0239
-0.0409
-0.2133
0.1267
0.3242
0.3329
-0.192
-0.0003
0.5939
-0.0064
-0.0218
0.5174
0.1271
0.3289
-18.8168
0.2633
25.3669
3
2.7428
1.6715
0.1083
0.6399
0.7609
0.9449
-0.0475
0.4341
-1.0795
-0.2243
-0.1696
0.081
0.5788
-0.0085
0.0001
1.3658
-0.1558
0.0378
0.5616
-0.1737
1.3647
-35.9529
-44.4685
36.5522
4
0.3844
0.2166
0.9705
-0.5076
1.4815
1.0145
-0.0896
-0.1634
0.909
-0.2548
0.0277
-0.7657
-0.3118
1.111
0.0001
2.0353
-0.0433
-0.1673
0.9995
0.0693
2.3785
-23.6753
-87.0348
42.4776
5
1.9385
-0.1681
-1.3367
2.7677
-2.3989
1.301
-0.3657
0.0045
0.1103
-0.2136
0.0281
-1.4982
-0.8087
0.1355
0
1.6514
0.2546
0.0282
0.7878
0.0528
1.2399
-28.4356
-129.1283
40.129
6
2.7168
0.4182
-0.6778
0.7747
0.558
0.1827
-0.163
-0.5454
-0.8631
0.5221
-0.0545
-0.5534
0.0199
0.6583
-0.0001
1.6378
0.4427
0.0878
1.0907
0.3561
1.7929
-10.691
-168.6969
47.0476
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
chain A and resid -2:94
A
-2 - 94
2
X-RAY DIFFRACTION
2
chainAandresid95:190
A
95 - 190
3
X-RAY DIFFRACTION
3
chainAandresid191:284
A
191 - 284
4
X-RAY DIFFRACTION
4
chainAandresid285:378
A
285 - 378
5
X-RAY DIFFRACTION
5
chainAandresid379:471
A
379 - 471
6
X-RAY DIFFRACTION
6
chainAandresid472:566
A
472 - 566
+
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