the biological assembly of BARF1 is a hexamer / the biological unit of M-CSF is a dimer
-
Components
#1: Protein
SecretedproteinBARF1 / 33 kDa early protein / p33
Mass: 22667.824 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus) Gene: BARF1 / Organ (production host): Human Embryonic Kidney cells / Production host: Homo sapiens (human) / References: UniProt: P0CW72
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.528 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26002
4499
5 %
RANDOM
Rwork
0.22163
-
-
-
obs
0.22353
85332
97.6 %
-
all
-
89831
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 45.47 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.47 Å2
0 Å2
-2.85 Å2
2-
-
-2.13 Å2
0 Å2
3-
-
-
5.77 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8075
0
159
442
8676
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.02
8453
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.374
1.967
11475
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.368
5
994
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.148
24.427
393
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.179
15
1437
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.049
15
39
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
1302
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
6304
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.567
1.5
5006
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.081
2
8146
X-RAY DIFFRACTION
r_scbond_it
1.861
3
3448
X-RAY DIFFRACTION
r_scangle_it
2.898
4.5
3332
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Refine-ID: X-RAY DIFFRACTION
Ens-ID
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
1
A
1492
mediumpositional
0.34
0.5
1
1
B
1492
mediumpositional
0.46
0.5
1
1
D
1492
mediumpositional
0.38
0.5
2
2
E
1187
mediumpositional
0.51
0.5
2
2
F
1187
mediumpositional
0.51
0.5
2
2
G
1187
mediumpositional
0.66
0.5
1
1
A
1492
mediumthermal
0.54
2
1
1
B
1492
mediumthermal
0.5
2
1
1
D
1492
mediumthermal
0.55
2
2
2
E
1187
mediumthermal
0.56
2
2
2
F
1187
mediumthermal
0.67
2
2
2
G
1187
mediumthermal
0.58
2
LS refinement shell
Resolution: 2.2→2.256 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.355
325
-
Rwork
0.382
5820
-
obs
-
-
92.09 %
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
3.4284
2.8362
1.0809
2.9242
0.7707
0.5843
0.2225
-0.3629
-0.0017
0.3008
-0.2427
-0.0573
0.0126
-0.142
0.0202
0.1239
-0.0066
0.0213
0.1412
-0.0058
0.02
14.026
-16.736
-14.068
2
0.7213
1.5204
0.1156
5.7108
-0.0461
0.0557
-0.0729
0.1343
-0.0582
-0.3753
0.0636
-0.2195
0.0051
0.0684
0.0093
0.1273
-0.0292
0.0316
0.1696
0.0327
0.0261
36.334
12.242
-25.044
3
4.0947
-1.0462
1.9554
0.5548
-0.4861
0.961
-0.1878
-0.4256
0.2116
0.1346
0.0694
0.132
-0.1403
-0.2364
0.1184
0.1788
-0.0011
0.0183
0.2365
-0.03
0.1382
14.787
39.9
-13.691
4
2.8666
-1.0196
1.6886
1.7143
-1.879
4.5218
0.2683
-0.5603
-0.3853
0.0706
-0.0002
0.2626
1.0672
-0.028
-0.2681
0.6044
0.0248
-0.053
0.3221
0.0238
0.1944
10.63
-56.005
-10.526
5
4.6945
-1.2277
-0.8392
1.6362
0.0835
0.9273
-0.0324
0.235
-0.2598
-0.3358
-0.0137
0.1154
0.1108
-0.0368
0.046
0.2004
-0.0476
0.0294
0.1723
-0.0114
0.0323
68.326
32.807
-18.599
6
1.0392
0.0819
0.4158
2.8385
1.7154
2.0364
-0.061
-0.1739
0.1098
0.0275
-0.0259
0.2455
-0.0665
-0.2602
0.087
0.1166
-0.0056
0.0437
0.2031
-0.0064
0.1165
47.138
55.996
4.754
7
63.185
-13.509
30.4882
59.3154
-42.714
37.9314
1.5386
1.1744
0.1484
-1.3649
-0.284
2.0718
1.3814
0.576
-1.2546
0.4289
0.1954
-0.1511
0.2505
-0.1524
0.2261
0.563
-10.009
-21.049
8
101.8406
-31.4252
33.739
53.9555
-32.6103
22.3578
0.7201
1.094
1.0018
0.171
-0.115
1.6803
-0.0052
0.2702
-0.6051
0.3463
0.1595
-0.1799
0.6157
-0.1864
0.3566
23.146
22.169
-28.665
9
0.5567
-0.0865
2.7481
28.9981
14.2756
21.3472
0.2177
-0.0459
0.002
-0.1205
-0.3865
-0.0053
0.9818
-0.4788
0.1688
0.1619
-0.0639
-0.0561
0.2718
-0.0173
0.4197
16.955
23.345
-14.764
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
20 - 219
2
X-RAY DIFFRACTION
2
B
20 - 219
3
X-RAY DIFFRACTION
3
D
20 - 219
4
X-RAY DIFFRACTION
4
E
2 - 146
5
X-RAY DIFFRACTION
5
F
2 - 146
6
X-RAY DIFFRACTION
6
G
2 - 146
7
X-RAY DIFFRACTION
7
A
301 - 303
8
X-RAY DIFFRACTION
8
B
301 - 303
9
X-RAY DIFFRACTION
9
D
301 - 303
+
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