There are two copies of the biologically relevant assembly in the asymmetric unit, comprising chains B,C and D (copy 1) and E, G, and H (copy 2). The correct oligomerization size and orientation of chains was determined experimentally in solution. Chains A and F correspond to crystallographic packing artefacts.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9795 Å / Relative weight: 1
Reflection
Resolution: 1.8→32.1 Å / Num. obs: 31718 / % possible obs: 68.2 % / Redundancy: 2 % / Biso Wilson estimate: 32.35 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.3
Reflection shell
Resolution: 1.8→1.85 Å / Redundancy: 0.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.9 / % possible all: 3.9
-
Processing
Software
Name
Version
Classification
BUSTER
2.10.2
refinement
XDS
datareduction
XSCALE
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.8→32.1 Å / Cor.coef. Fo:Fc: 0.9408 / Cor.coef. Fo:Fc free: 0.9244 / SU R Cruickshank DPI: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.172
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2392
1600
5.04 %
RANDOM
Rwork
0.2108
-
-
-
obs
0.2123
31718
67.84 %
-
Displacement parameters
Biso mean: 51.24 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-6.2821 Å2
0 Å2
0 Å2
2-
-
1.2079 Å2
0 Å2
3-
-
-
5.0742 Å2
Refine analyze
Luzzati coordinate error obs: 0.3 Å
Refinement step
Cycle: LAST / Resolution: 1.8→32.1 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3647
0
25
249
3921
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
3708
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.96
4984
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1455
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
170
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
496
HARMONIC
5
X-RAY DIFFRACTION
t_it
3708
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.2
X-RAY DIFFRACTION
t_other_torsion
18.8
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
497
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
4521
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.8→1.86 Å / Total num. of bins used: 16
Rfactor
Num. reflection
% reflection
Rfree
0.3087
12
6.49 %
Rwork
0.2103
173
-
all
0.2153
185
-
obs
-
-
4.35 %
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
3.1949
0.226
1.3692
2.0987
-1.8103
9.9416
-0.1545
0.3458
-0.3282
-0.021
0.0347
-0.1093
0.2702
0.1102
0.1197
-0.242
0.0497
0.0028
-0.1009
-0.0807
-0.0997
14.2946
21.281
43.9163
2
2.4401
0.7066
2.0089
2.4972
0.865
9.6432
-0.0183
-0.0074
-0.1079
0.2448
-0.0021
-0.1264
0.3561
0.1292
0.0204
-0.3511
0.0046
-0.0027
-0.2576
-0.0458
-0.2232
19.1268
26.841
57.8562
3
0.1287
-0.1509
-0.7322
0.7899
1.9626
11.969
-0.0239
-0.05
-0.0728
0.0275
0.054
0.0283
-0.0079
0.2437
-0.0301
-0.4014
0.0302
-0.0164
-0.148
-0.0637
-0.2069
29.1925
31.5397
59.434
4
1.0905
-0.0421
-0.3265
0.6864
1.4753
14.0407
0.0945
0.0285
0.0654
-0.0278
0.0862
-0.0274
-0.6281
-0.1857
-0.1807
-0.3592
0.0319
-0.0071
-0.2955
-0.0474
-0.2291
18.9409
35.1381
63.4761
5
2.4263
-0.1042
-2.1548
3.5569
0.3096
6.1472
-0.006
-0.1135
0.0701
-0.4031
0.1027
-0.1899
-0.6183
0.2015
-0.0967
-0.4281
-0.0402
0.0046
-0.1911
-0.0893
-0.2204
42.691
25.8986
30.2486
6
2.3804
-0.307
-0.3085
1.6323
-0.2824
9.352
-0.1514
-0.0776
0.3697
0.0162
-0.0554
-0.0665
-0.5922
0.6906
0.2068
-0.1335
-0.037
0.0163
-0.0472
-0.0082
-0.0836
37.6759
30.1012
45.4554
7
0.691
-0.2978
-0.8852
0.4164
0.2634
9.3625
0.0917
0.0083
-0.0178
-0.0323
0.1114
0.0384
0.2625
-0.0715
-0.2031
-0.2763
-0.0494
-0.0009
-0.2144
-0.0421
-0.1915
41.9516
18.5845
24.0675
8
0.1043
0.0262
2.0533
0.6463
2.1014
12.6869
-0.0264
-0.0899
0.0961
-0.0057
-0.0178
0.0383
0.1018
0.2253
0.0442
-0.315
-0.0406
0.0101
-0.0262
-0.0799
-0.1967
52.3323
21.0982
27.8978
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|129 - A|175 }
2
X-RAY DIFFRACTION
2
{ B|129 - B|179 }
3
X-RAY DIFFRACTION
3
{ C|123 - C|179 }
4
X-RAY DIFFRACTION
4
{ D|124 - D|179 }
5
X-RAY DIFFRACTION
5
{ E|127 - E|179 }
6
X-RAY DIFFRACTION
6
{ F|127 - F|176 }
7
X-RAY DIFFRACTION
7
{ G|124 - G|179 }
8
X-RAY DIFFRACTION
8
{ H|123 - H|179 }
+
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