RNA polymerase III cis-regulatory region sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase III / DNA binding / nucleus / cytoplasm / cytosol Similarity search - Function
Resolution: 2.4→42.62 Å / Num. obs: 13629 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 49.71 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.5
Reflection shell
Resolution: 2.4→2.53 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
SCALA
datascaling
SHARP
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.4→33.29 Å / SU ML: 0.32 / σ(F): 0.91 / Phase error: 24.17 / Stereochemistry target values: ML Details: THE HYDROGEN ATOMS ON THE SULPHUR ATOMS O OF MERCURY-BOUND CYSTEINES HAVE BEEN REMOVED AFTER REFINEMENT AS THEY DO NOT MAKE SENSE CHEMICALLY.
Rfactor
Num. reflection
% reflection
Rfree
0.2236
1223
5 %
Rwork
0.1809
-
-
obs
0.183
13591
99.85 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 55.97 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→33.29 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1531
0
2
42
1575
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.011
1566
X-RAY DIFFRACTION
f_angle_d
1.237
2113
X-RAY DIFFRACTION
f_dihedral_angle_d
15.234
588
X-RAY DIFFRACTION
f_chiral_restr
0.074
235
X-RAY DIFFRACTION
f_plane_restr
0.006
279
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.4-2.4961
0.3118
120
0.2836
2595
X-RAY DIFFRACTION
99
2.4961-2.6096
0.3171
142
0.2638
2573
X-RAY DIFFRACTION
100
2.6096-2.7471
0.2713
153
0.2259
2582
X-RAY DIFFRACTION
100
2.7471-2.9192
0.3071
131
0.2141
2584
X-RAY DIFFRACTION
100
2.9192-3.1444
0.249
127
0.1868
2607
X-RAY DIFFRACTION
100
3.1444-3.4605
0.2396
163
0.1752
2539
X-RAY DIFFRACTION
100
3.4605-3.9606
0.1863
128
0.1606
2603
X-RAY DIFFRACTION
100
3.9606-4.9872
0.1776
146
0.1436
2584
X-RAY DIFFRACTION
100
4.9872-33.2928
0.2172
113
0.1852
2613
X-RAY DIFFRACTION
100
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
0.0062
-0.043
0.0309
0.0195
-0.0094
0.0236
-0.2313
-0.5589
0.5021
-0.0953
-0.2888
0.0054
-0.0839
0.0146
0.0007
0.4575
-0.0737
-0.0467
0.5193
0.0481
0.5888
9.9169
19.0034
16.2428
2
0.2426
0.2145
-0.0037
0.1853
-0.1393
0.2867
0.0551
0.0919
-0.279
-0.2038
-0.0424
0.0974
0.4433
0.1364
0.0001
0.4901
0.0757
-0.0363
0.3857
0.0101
0.4743
32.614
6.7174
21.9338
3
0.1129
0.0115
-0.0692
0.0211
-0.0339
0.0445
-0.3161
-0.1996
-0.0813
0.7175
0.3771
-0.3629
0.4608
-0.5415
-0.0004
0.3798
-0.1144
-0.0135
0.5334
-0.012
0.4634
24.835
9.7706
32.1804
4
-0.006
0.0315
-0.0565
0.0489
-0.0405
-0.009
-0.1249
-0.2917
-0.0671
-0.1707
0.3772
0.1774
-0.2435
-0.274
-0
0.4455
0.0674
0.0007
0.435
0.0071
0.4873
31.2106
15.7643
33.5008
5
-0.0165
-0.049
0.01
0.0401
0.0212
0.0076
0.2065
-0.2293
0.0462
-0.1429
-0.2958
-0.4386
0.0557
-0.0666
0.0003
0.3719
-0.0607
-0.0801
0.3473
0.0102
0.4815
45.4521
4.0451
26.6265
6
0.0191
-0.0099
0.0132
0.034
-0.0165
-0.0051
-0.063
-0.0273
0.2396
-0.1416
0.0555
-0.1901
-0.1185
-0.2047
-0.0002
0.4345
0.0413
-0.033
0.4911
-0.0252
0.4257
47.2902
10.2038
30.2506
7
0.0325
-0.0149
-0.0149
0.1031
-0.0097
0.0016
-0.0682
0.297
0.222
-0.1418
-0.0328
-0.4226
-0.0548
0.1272
-0.0001
0.3968
0.0704
-0.0513
0.4528
0.0157
0.3843
28.4311
23.4516
23.566
8
0.0058
0.0466
0.025
0.0122
0.0761
0.0343
0.4236
0.5045
-0.1169
-0.5072
0.1345
-0.6061
0.3401
-0.2648
-0
0.6712
-0.0527
-0.1415
0.4739
-0.0707
0.4661
16.4919
11.3077
6.98
9
0.0504
-0.1439
0.0678
0.2791
-0.1178
0.026
-0.0868
0.1753
0.0759
0.0286
0.127
0.1379
0.089
0.0016
0.0001
0.3546
-0.0644
-0.0499
0.419
0.0363
0.4497
20.2239
17.3079
19.1751
10
-0.0056
-0.0003
-0.0576
0.0054
-0.0368
0.027
-0.7494
0.0278
0.1782
0.1557
-0.4495
-0.8383
-0.229
-0.2635
0.0016
0.4686
0.0199
-0.0508
0.5107
0.093
0.6421
42.3179
17.3443
19.2485
11
2.1056
0.8807
0.5425
2.031
1.193
2.2821
-0.02
0.2624
-0.0826
0.1206
0.1372
0.1687
0.3279
0.0686
-0.1758
0.3843
-0.0263
-0.0623
0.445
0.0273
0.4021
19.557
20.6061
10.7177
12
0.0684
0.3436
0.9351
0.1424
-0.1016
0.735
-0.0114
0.1712
-0.0263
-0.1014
-0.0952
-0.0118
0.0033
0.0265
0.0001
0.4691
0.0214
-0.0103
0.4326
0.0184
0.4232
24.5336
21.1901
10.0452
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAAND (RESID3THROUGH9 )
2
X-RAY DIFFRACTION
2
CHAINAAND (RESID10THROUGH32 )
3
X-RAY DIFFRACTION
3
CHAINAAND (RESID33THROUGH45 )
4
X-RAY DIFFRACTION
4
CHAINAAND (RESID46THROUGH54 )
5
X-RAY DIFFRACTION
5
CHAINAAND (RESID55THROUGH59 )
6
X-RAY DIFFRACTION
6
CHAINAAND (RESID60THROUGH68 )
7
X-RAY DIFFRACTION
7
CHAINAAND (RESID69THROUGH75 )
8
X-RAY DIFFRACTION
8
CHAINAAND (RESID76THROUGH85 )
9
X-RAY DIFFRACTION
9
CHAINAAND (RESID86THROUGH98 )
10
X-RAY DIFFRACTION
10
CHAINAAND (RESID99THROUGH108 )
11
X-RAY DIFFRACTION
11
CHAINBAND (RESID7THROUGH51 )
12
X-RAY DIFFRACTION
12
CHAINBAND (RESID52THROUGH100 )
+
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