A: ANCILLARY PROTEIN 2 B: ANCILLARY PROTEIN 2 C: ANCILLARY PROTEIN 2 D: ANCILLARY PROTEIN 2 E: ANCILLARY PROTEIN 2 F: ANCILLARY PROTEIN 2 G: ANCILLARY PROTEIN 2 H: ANCILLARY PROTEIN 2 I: ANCILLARY PROTEIN 2 J: ANCILLARY PROTEIN 2 K: ANCILLARY PROTEIN 2 L: ANCILLARY PROTEIN 2 hetero molecules
Mass: 24878.572 Da / Num. of mol.: 12 / Fragment: N-TERMINAL DOMAIN, RESIDUES 8-222 Source method: isolated from a genetically manipulated source Details: COVALENT SPERMIDINE CROSS-LINK BETWEEN Q211 OF A AND B, C AND D, E AND F, G AND H, I AND J, K AND L Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: 90/306S / Description: NEW ZEALAND / Plasmid: PPROEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S5FV19
Mass: 18.015 Da / Num. of mol.: 985 / Source method: isolated from a natural source / Formula: H2O
-
Details
Nonpolymer details
SPERMIDINE (SPD): COVALENT LINK WITH GLN 211
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.26 Å3/Da / Density % sol: 42.4 % Description: STRUCTURE WAS SOLVED USING MAD USING A SELENOMETHIONINE-DERIVATIVE. INITIAL MODEL WAS USED TO SOLVE THE NATIVE DATASET USED FOR BUILDING OF FINAL MODEL.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9537 Å / Relative weight: 1
Reflection
Resolution: 2→47.91 Å / Num. obs: 1069788 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 36.14 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.94
Reflection shell
Resolution: 2→2 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.5 / % possible all: 100
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Processing
Software
Name
Version
Classification
BUSTER
2.11.5
refinement
XDS
datareduction
SCALA
datascaling
autoSHARP
phasing
Refinement
Method to determine structure: MAD Starting model: NONE Resolution: 2→47.5 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.9277 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.16 Details: CHAINS A, B, C, D, E, F, G, H IN RELIABLE ELECTRON DENSITY. CHAINS K, L LESS SO. CHAINS K, L WERE MODELLED BASED ON CHAIN A.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.232
9223
5.12 %
RANDOM
Rwork
0.2013
-
-
-
obs
0.2026
180308
99.96 %
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Displacement parameters
Biso mean: 49.57 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.1959 Å2
0 Å2
0 Å2
2-
-
-2.1959 Å2
0 Å2
3-
-
-
4.3919 Å2
Refine analyze
Luzzati coordinate error obs: 0.307 Å
Refinement step
Cycle: LAST / Resolution: 2→47.5 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
20385
0
107
985
21477
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
21104
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.05
28594
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
7391
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
685
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
2913
HARMONIC
5
X-RAY DIFFRACTION
t_it
21104
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.18
X-RAY DIFFRACTION
t_other_torsion
18.12
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
2637
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
24168
SEMIHARMONIC
4
LS refinement shell
Resolution: 2→2.05 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2417
1131
8.54 %
Rwork
0.2206
12116
-
all
0.2224
13247
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obs
-
-
99.96 %
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
1.6757
-0.3866
0.2659
1.4944
-0.2188
2.1068
0.0179
0.1338
-0.1186
-0.0508
-0.0531
-0.0793
0.2294
0.3041
0.0352
-0.0518
0.0798
0.0064
0.0101
-0.0398
-0.1339
-47.501
23.0293
67.1496
2
2.5898
0.5874
-0.5866
2.613
-1.1598
3.1185
-0.3599
-0.2037
-0.5335
-0.0147
-0.0583
-0.3469
0.2799
-0.1172
0.4182
-0.1259
0.0648
0.1191
-0.206
0.03
-0.0116
-24.4325
-3.3749
43.8526
3
1.4742
-0.5486
-0.0151
1.9263
0.0065
3.8068
0.0151
0.2425
0.2555
-0.097
-0.0637
0.0813
-0.4574
-0.6961
0.0486
-0.2554
0.0354
-0.0502
0.0287
-0.0323
-0.0642
-16.6066
16.7835
99.4152
4
1.3172
-0.0093
1.1818
1.2905
-0.0865
3.4379
0.1986
0.1691
-0.2287
0.0301
0.1248
-0.1068
0.5997
0.4216
-0.3235
-0.0236
0.0783
-0.0617
-0.08
-0.0967
-0.1257
-47.0968
23.141
-1.7722
5
3.7814
0.3674
0.4813
1.2821
0.4843
2.5049
-0.0452
0.0653
-0.2024
0.1441
-0.1183
0.218
0.3712
-0.2638
0.1635
-0.182
-0.0231
0.0487
-0.1066
-0.1206
-0.0115
-23.2977
-4.5918
114.601
6
2.1634
0.4565
-0.5211
4.6108
-1.8645
2.7976
-0.2448
0.0864
0.0132
0.0223
-0.1766
-0.5565
-0.3243
0.0548
0.4214
-0.111
-0.0074
-0.0523
-0.2208
0.0339
-0.1081
-16.586
18.1283
29.7719
7
2.2916
-0.7265
-0.7195
2.1628
0.4946
2.9245
0.2225
0.0902
0.3656
-0.2012
-0.0339
-0.3804
-0.5489
0.3506
-0.1886
-0.0525
-0.0734
0.0332
-0.1146
-0.0085
-0.1318
-43.1778
45.2603
81.8208
8
2.1453
-0.1009
-0.1275
2.3729
-0.2264
2.084
0.0737
0.0798
-0.1331
0.0107
0.074
0.4647
-0.2418
-0.1852
-0.1477
-0.0643
0.007
-0.0471
-0.1425
0.0482
-0.0599
-23.6139
71.5419
108.23
9
4.1458
0.4244
-0.0199
1.4704
0.7049
3.3483
0.1363
-0.6551
-1.2105
0.2453
-0.0591
-0.0799
0.6457
0.0455
-0.0772
-0.1416
-0.0106
-0.1057
-0.2423
0.2392
0.0278
-9.3788
53.5831
53.9036
10
2.162
0.1277
0.5082
1.125
0.1521
2.3543
-0.148
0.1027
0.1516
0.0422
0.1537
-0.1795
-0.1773
0.3644
-0.0057
-0.1016
-0.0282
-0.0161
-0.0177
-0.0407
-0.0929
-42.8837
45.5308
12.7708
11
2.9549
-0.2832
-0.8865
1.8969
1.1894
3.7445
0.1939
0.0492
-0.1057
-0.1099
-0.2785
0.2256
-0.5088
-0.4179
0.0845
-0.0619
0.0791
-0.0583
-0.1137
-0.0079
-0.1504
-23.8187
71.0382
39.5648
12
2.0754
0.2412
0.2227
2.2997
0.6008
2.7208
-0.002
0.0475
-0.3552
0.0119
0.1086
0.0945
0.2361
0.3353
-0.1065
-0.1441
0.0398
-0.0053
-0.0706
0.0481
-0.0622
-9.5616
54.201
123.38
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
3
X-RAY DIFFRACTION
3
CHAINC
4
X-RAY DIFFRACTION
4
CHAIND
5
X-RAY DIFFRACTION
5
CHAINE
6
X-RAY DIFFRACTION
6
CHAINF
7
X-RAY DIFFRACTION
7
CHAING
8
X-RAY DIFFRACTION
8
CHAINH
9
X-RAY DIFFRACTION
9
CHAINI
10
X-RAY DIFFRACTION
10
CHAINJ
11
X-RAY DIFFRACTION
11
CHAINK
12
X-RAY DIFFRACTION
12
CHAINL
+
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