Mass: 49064.035 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76RI7
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9786 Å / Relative weight: 1
Reflection
Resolution: 2.42→48.36 Å / Num. obs: 229532 / % possible obs: 99.1 % / Redundancy: 13.3 % / CC1/2: 0.998 / Χ2: 0.93 / Net I/σ(I): 10.4
Reflection shell
Resolution: 2.42→2.48 Å / Num. unique obs: 14955 / CC1/2: 0.352 / % possible all: 88.1
-
Processing
Software
Name
Version
Classification
BUSTER
2.10.4
refinement
XDS
datareduction
XDS
datascaling
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.422→48.36 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.515 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.544 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.275
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2348
8712
-
RANDOM
Rwork
0.2069
-
-
-
obs
0.2083
174243
75.8 %
-
Displacement parameters
Biso mean: 60.87 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.919 Å2
0 Å2
0 Å2
2-
-
-0.0547 Å2
0 Å2
3-
-
-
-4.8643 Å2
Refine analyze
Luzzati coordinate error obs: 0.34 Å
Refinement step
Cycle: LAST / Resolution: 2.422→48.36 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
31860
0
80
1980
33920
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.006
32747
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.81
44538
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
10905
SINUSOIDAL
2
X-RAY DIFFRACTION
t_gen_planes
5501
HARMONIC
5
X-RAY DIFFRACTION
t_it
32747
HARMONIC
10
X-RAY DIFFRACTION
t_chiral_improper_torsion
4264
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_ideal_dist_contact
24977
SEMIHARMONIC
4
X-RAY DIFFRACTION
t_omega_torsion
2.51
X-RAY DIFFRACTION
t_other_torsion
15.97
LS refinement shell
Resolution: 2.422→2.48 Å
Rfactor
Num. reflection
% reflection
Rfree
0.3229
172
-
Rwork
0.2774
-
-
obs
-
-
22.89 %
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
1.1736
0.2579
-0.2139
1.3747
-0.773
5.2841
0.0347
0.1579
-0.1961
0.1579
-0.0449
-0.0705
-0.1961
-0.0705
0.0102
-0.0409
0.0625
0.0254
-0.1204
-0.0209
-0.1219
-117.969
21.035
-12.9848
2
1.314
-0.0775
0.5563
1.6128
-0.3678
3.3292
-0.0056
0.4743
-0.1407
0.4743
0.073
0.0089
-0.1407
0.0089
-0.0673
0.2059
0.2595
0.0261
0.0666
0.0171
-0.1544
-164.576
19.2724
-2.0861
3
1.3494
-0.271
0.2855
3.3727
-1.4561
3.1491
-0.0345
-0.215
-0.2317
-0.215
-0.1365
0.3651
-0.2317
0.3651
0.171
0.0262
-0.0729
0.0167
-0.0165
0.0577
-0.0538
-167.047
45.4538
-75.157
4
0.9982
0.2487
-0.1832
4.653
-0.0018
3.0977
-0.1398
-0.009
0.4159
-0.009
0.0558
-0.0499
0.4159
-0.0499
0.084
-0.0865
-0.0012
0.038
-0.0312
-0.1242
-0.0045
-121.977
-17.5804
-40.6802
5
1.3736
0.222
0.1621
4.5004
-0.119
2.8483
-0.0774
0.3544
-0.583
0.3544
0.031
0.0022
-0.583
0.0022
0.0464
0.1447
0.0886
-0.0719
-0.0252
0.0027
-0.0287
-114.156
59.9173
-41.127
6
1.5323
-0.1361
0.8203
2.5308
0.4087
5.9567
0.164
-0.3639
0.5679
-0.3639
-0.059
0.3932
0.5679
0.3932
-0.105
-0.0425
0.0967
-0.0016
0.0391
-0.0809
-0.0864
-165.079
-2.6114
-76.549
7
0.9948
0.0865
0.248
4.1411
1.7111
3.5755
-0.2384
-0.2378
-0.6495
-0.2378
0.2179
0.4211
-0.6495
0.4211
0.0206
0.1228
-0.0358
-0.1288
0.0175
-0.0447
-0.0383
-166.745
59.1385
-28.7143
8
0.9981
-0.2146
-0.1921
2.7574
1.0687
5.6747
0.0063
0.0349
0.3776
0.0349
-0.0972
0.0616
0.3776
0.0616
0.091
-0.1014
-0.1266
-0.0392
0.1719
-0.131
-0.0268
-117.523
-3.1143
-86.9965
9
1.0766
0.1158
-0.0052
5.7895
0.436
1.8932
-0.1165
0.4119
0.2106
0.4119
0.2849
-0.1139
0.2106
-0.1139
-0.1684
-0.1112
0.0674
0.0134
0.0105
-0.0006
0.0083
-163.131
-19.3851
-31.463
10
1.1261
-0.0873
-0.2835
3.9977
-1.4123
2.5349
-0.0193
-0.4502
0.0079
-0.4502
0.0501
-0.3041
0.0079
-0.3041
-0.0308
0.1133
0.0093
-0.0933
0.1217
0.0034
-0.0634
-111.558
45.1636
-87.1052
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{ A|126 - A|550 A|601 - A|602 }
A
126 - 550
2
X-RAY DIFFRACTION
1
{ A|126 - A|550 A|601 - A|602 }
A
601 - 602
3
X-RAY DIFFRACTION
2
{ B|126 - B|550 B|601 - B|602 }
B
126 - 550
4
X-RAY DIFFRACTION
2
{ B|126 - B|550 B|601 - B|602 }
B
601 - 602
5
X-RAY DIFFRACTION
3
{ C|126 - C|550 C|601 - C|602 }
C
126 - 550
6
X-RAY DIFFRACTION
3
{ C|126 - C|550 C|601 - C|602 }
C
601 - 602
7
X-RAY DIFFRACTION
4
{ D|126 - D|550 D|601 - D|602 }
D
126 - 550
8
X-RAY DIFFRACTION
4
{ D|126 - D|550 D|601 - D|602 }
D
601 - 602
9
X-RAY DIFFRACTION
5
{ E|126 - E|550 E|601 - E|602 }
E
126 - 550
10
X-RAY DIFFRACTION
5
{ E|126 - E|550 E|601 - E|602 }
E
601 - 602
11
X-RAY DIFFRACTION
6
{ F|126 - F|550 F|601 - F|602 }
F
126 - 550
12
X-RAY DIFFRACTION
6
{ F|126 - F|550 F|601 - F|602 }
F
601 - 602
13
X-RAY DIFFRACTION
7
{ G|126 - G|550 G|601 - G|602 }
G
126 - 550
14
X-RAY DIFFRACTION
7
{ G|126 - G|550 G|601 - G|602 }
G
601 - 602
15
X-RAY DIFFRACTION
8
{ H|126 - H|550 H|601 - H|602 }
H
126 - 550
16
X-RAY DIFFRACTION
8
{ H|126 - H|550 H|601 - H|602 }
H
601 - 602
17
X-RAY DIFFRACTION
9
{ I|126 - I|550 I|601 - I|602 }
I
126 - 550
18
X-RAY DIFFRACTION
9
{ I|126 - I|550 I|601 - I|602 }
I
601 - 602
19
X-RAY DIFFRACTION
10
{ J|126 - J|550 J|601 - J|602 }
J
126 - 550
20
X-RAY DIFFRACTION
10
{ J|126 - J|550 J|601 - J|602 }
J
601 - 602
+
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