0.023856
0.013773
0.000000
0.000000
0.027546
0.000000
0.000000
0.000000
0.014610
0.000000
0.000000
0.000000
Ovaere, M.
Van Meervelt, L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.000
90.000
120.000
41.919
41.919
68.444
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
C12 H16 N5 O5 P
341.260
[(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE
DNA linking
C11 H16 N3 O6 P
317.235
n
[(1R,4S,6S)-4-(4-amino-2-oxopyrimidin-1(2H)-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen phosphate
DNA linking
C12 H16 N5 O6 P
357.259
n
[(1R,4S,6S)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen phosphate
DNA linking
C12 H17 N2 O7 P
332.246
n
[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate
DNA linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
N
C
N
84
R
C
N
85
N
N
N
86
N
C
N
87
N
O
N
88
N
N
N
89
N
C
N
90
N
O
N
91
N
C
N
92
N
C
N
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
O
N
110
N
P
N
111
N
O
N
112
N
O
N
113
N
O
N
114
N
C
N
115
R
C
N
116
N
O
N
117
S
C
N
118
N
O
N
119
R
C
N
120
N
O
N
121
R
C
Y
122
N
N
Y
123
N
C
Y
124
N
N
Y
125
N
C
N
126
N
C
N
127
N
O
N
128
N
N
N
129
N
C
N
130
N
N
N
131
N
N
Y
132
N
C
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
MG
N
151
N
O
N
152
N
P
N
153
N
O
N
154
N
O
N
155
N
O
N
156
N
C
N
157
R
C
N
158
N
O
N
159
S
C
N
160
N
O
N
161
R
C
N
162
N
O
N
163
R
C
N
164
N
N
N
165
N
C
N
166
N
O
N
167
N
N
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
C
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
O
N
186
N
O
N
187
N
P
N
188
N
O
N
189
N
O
N
190
N
C
N
191
R
C
N
192
S
C
N
193
N
O
N
194
N
C
N
195
S
C
N
196
N
C
N
197
N
C
Y
198
N
N
Y
199
N
C
Y
200
N
N
Y
201
N
C
Y
202
N
C
Y
203
N
N
Y
204
N
C
N
205
N
N
Y
206
N
N
Y
207
N
C
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
P
N
225
N
N
N
226
N
C
N
227
N
O
N
228
N
N
N
229
N
C
N
230
N
N
N
231
N
C
N
232
N
C
N
233
S
C
N
234
N
C
N
235
S
C
N
236
N
O
N
237
R
C
N
238
N
C
N
239
N
O
N
240
N
C
N
241
N
C
N
242
N
O
N
243
N
O
N
244
N
O
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
P
N
262
N
N
N
263
N
C
N
264
N
N
N
265
N
N
Y
266
N
C
Y
267
N
C
N
268
N
C
N
269
N
O
Y
270
N
N
Y
271
N
C
Y
272
N
N
N
273
S
C
N
274
N
C
N
275
S
C
N
276
N
O
N
277
R
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
C
N
282
N
O
N
283
N
O
N
284
N
O
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
O
N
302
R
C
N
303
N
C
N
304
N
C
N
305
S
C
N
306
N
O
N
307
N
C
N
308
N
C
N
309
N
C
N
310
N
C
N
311
N
N
N
312
N
C
N
313
N
O
N
314
N
N
N
315
N
C
N
316
S
C
N
317
N
P
N
318
N
O
N
319
N
O
N
320
N
O
N
321
N
C
N
322
N
O
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
Y
137
N
sing
Y
138
N
sing
Y
139
N
doub
N
140
N
sing
Y
141
N
sing
N
142
N
sing
Y
143
N
doub
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
doub
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
doub
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
doub
N
214
N
sing
N
215
N
sing
Y
216
N
sing
Y
217
N
sing
Y
218
N
doub
N
219
N
sing
Y
220
N
sing
Y
221
N
doub
Y
222
N
sing
Y
223
N
sing
Y
224
N
doub
Y
225
N
doub
N
226
N
sing
N
227
N
sing
N
228
N
sing
Y
229
N
sing
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
doub
N
240
N
doub
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
doub
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
doub
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
doub
N
278
N
sing
N
279
N
sing
N
280
N
sing
Y
281
N
doub
Y
282
N
sing
N
283
N
sing
Y
284
N
sing
N
285
N
doub
Y
286
N
doub
Y
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
doub
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
doub
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
doub
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
doub
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
doub
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
doub
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
GE
Chemistry
0947-6539
17
7823
7830
10.1002/chem.201003594
21618623
The Crystal Structure of the CeNA:RNA Hybrid ce(GCGTAGCG):r(CGCUACGC).
2011
10.2210/pdb3knc/pdb
pdb_00003knc
100
1
CCD
2008-09-29
MARMOSAIC 225 mm CCD
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
X06DA
SLS
1.0000
SYNCHROTRON
SLS BEAMLINE X06DA
CeNA
2887.177
5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR)P*(XGR)P*(XGR))-3'
1
syn
polymer
RNA
2501.553
5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'
1
syn
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
18.015
water
47
nat
water
no
yes
(XGR)(XCR)(XGR)(XTR)(XAR)(XGR)(XCR)(XGR)(XGR)
GCGTNGCGG
A
polydeoxyribonucleotide
no
no
CGCUACGC
CGCUACGC
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
3.22
61.82
The structure factor file contains Friedel pairs
VAPOR DIFFUSION, HANGING DROP
0.2M Magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
289
Magnesium formate
1
Magnesium formate
2
1.753
1
19
A
1
B
8
1.052
A_XGR1:C8_B
1
-12.277
0.061
0.545
-0.125
-5.102
1
19
A
2
B
7
1.030
A_XCR2:G7_B
2
-12.505
0.005
0.521
-0.244
-9.561
1
19
A
3
B
6
5.729
A_XGR3:C6_B
3
-14.167
-0.165
0.317
0.080
-8.304
1
20
A
4
B
5
-2.908
A_XTR4:A5_B
4
-13.046
0.375
0.439
-0.121
-2.720
1
19
A
6
B
3
-5.217
A_XGR6:C3_B
5
-11.560
-0.063
-0.065
-0.279
-3.273
1
19
A
7
B
2
0.859
A_XCR7:G2_B
6
-10.283
-0.466
0.191
-0.086
-9.236
1
19
A
8
B
1
5.307
A_XGR8:C1_B
7
-15.039
-0.473
-0.252
0.018
3.065
35.251
A
A
1
2
5.050
B
B
8
7
3.270
3.054
-0.159
-2.349
AA_XGR1XCR2:G7C8_BB
1
-1.344
2.222
35.098
-4.319
0.069
2.487
32.155
A
A
2
3
15.881
B
B
7
6
3.125
8.686
-0.151
-1.941
AA_XCR2XGR3:C6G7_BB
2
2.134
-3.901
30.917
-4.865
0.607
2.787
36.317
A
A
3
4
10.348
B
B
6
5
3.143
6.416
-0.415
-1.691
AA_XGR3XTR4:A5C6_BB
3
1.632
-2.631
35.729
-3.532
0.874
3.873
65.770
A
A
4
6
27.077
B
B
5
3
5.819
28.602
0.181
-3.741
AA_XTR4XGR6:C3A5_BB
4
3.937
-3.727
59.744
-5.281
0.086
2.983
29.035
A
A
6
7
10.479
B
B
3
2
3.382
5.223
0.957
-2.249
AA_XGR6XCR7:G2C3_BB
5
1.749
-3.508
28.518
-5.613
-1.531
2.029
32.941
A
A
7
8
25.197
B
B
2
1
3.246
13.860
-0.250
-2.222
AA_XCR7XGR8:C1G2_BB
6
1.636
-2.974
29.913
-5.921
0.678
software
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Other
Refinement description
Database references
Derived calculations
Data collection
1
0
2010-12-08
1
1
2011-07-13
1
2
2012-02-01
1
3
2017-11-01
1
4
2021-10-13
1
5
2024-02-21
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr2_auth_seq_id
_struct_ref_seq.db_align_beg
_struct_ref_seq.db_align_end
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2009-11-12
REL
REL
MG
MAGNESIUM ION
HOH
water
The CeNA strand was synthesized.
sample
The RNA strand was synthesized.
sample
MG
100
3
MG
MG
100
A
MG
200
3
MG
MG
200
A
HOH
14
4
HOH
HOH
14
A
HOH
15
4
HOH
HOH
15
A
HOH
17
4
HOH
HOH
17
A
HOH
20
4
HOH
HOH
20
A
HOH
22
4
HOH
HOH
22
A
HOH
23
4
HOH
HOH
23
A
HOH
24
4
HOH
HOH
24
A
HOH
25
4
HOH
HOH
25
A
HOH
28
4
HOH
HOH
28
A
HOH
33
4
HOH
HOH
33
A
HOH
34
4
HOH
HOH
34
A
HOH
35
4
HOH
HOH
35
A
HOH
101
4
HOH
HOH
101
A
HOH
102
4
HOH
HOH
102
A
HOH
103
4
HOH
HOH
103
A
HOH
104
4
HOH
HOH
104
A
HOH
105
4
HOH
HOH
105
A
HOH
106
4
HOH
HOH
106
A
HOH
1
4
HOH
HOH
107
A
HOH
3
4
HOH
HOH
108
A
HOH
4
4
HOH
HOH
109
A
HOH
7
4
HOH
HOH
110
A
HOH
8
4
HOH
HOH
111
A
HOH
201
4
HOH
HOH
201
A
HOH
202
4
HOH
HOH
202
A
HOH
203
4
HOH
HOH
203
A
HOH
204
4
HOH
HOH
204
A
HOH
205
4
HOH
HOH
205
A
HOH
206
4
HOH
HOH
206
A
HOH
9
4
HOH
HOH
9
B
HOH
10
4
HOH
HOH
10
B
HOH
11
4
HOH
HOH
11
B
HOH
12
4
HOH
HOH
12
B
HOH
13
4
HOH
HOH
13
B
HOH
2
4
HOH
HOH
14
B
HOH
5
4
HOH
HOH
15
B
HOH
16
4
HOH
HOH
16
B
HOH
6
4
HOH
HOH
17
B
HOH
18
4
HOH
HOH
18
B
HOH
19
4
HOH
HOH
19
B
HOH
21
4
HOH
HOH
21
B
HOH
26
4
HOH
HOH
26
B
HOH
27
4
HOH
HOH
27
B
HOH
29
4
HOH
HOH
29
B
HOH
30
4
HOH
HOH
30
B
HOH
31
4
HOH
HOH
31
B
HOH
32
4
HOH
HOH
32
B
31.370
2.500
2.500
24.900
24.900
Phaser MODE: MR_AUTO
XGR
1
n
1
XGR
1
A
XCR
2
n
2
XCR
2
A
XGR
3
n
3
XGR
3
A
XTR
4
n
4
XTR
4
A
XAR
5
n
5
XAR
5
A
XGR
6
n
6
XGR
6
A
XCR
7
n
7
XCR
7
A
XGR
8
n
8
XGR
8
A
XGR
9
n
9
XGR
9
A
C
1
n
1
C
1
B
G
2
n
2
G
2
B
C
3
n
3
C
3
B
U
4
n
4
U
4
B
A
5
n
5
A
5
B
C
6
n
6
C
6
B
G
7
n
7
G
7
B
C
8
n
8
C
8
B
author_and_software_defined_assembly
PISA
2
dimeric
1280
-34.1
11444
A
HOH
101
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
102
E
O
HOH
1_555
176.6
A
HOH
101
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
103
E
O
HOH
1_555
92.0
A
HOH
102
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
103
E
O
HOH
1_555
86.0
A
HOH
101
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
104
E
O
HOH
1_555
92.6
A
HOH
102
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
104
E
O
HOH
1_555
90.0
A
HOH
103
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
104
E
O
HOH
1_555
90.3
A
HOH
101
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
105
E
O
HOH
1_555
90.9
A
HOH
102
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
105
E
O
HOH
1_555
86.5
A
HOH
103
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
105
E
O
HOH
1_555
90.9
A
HOH
104
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
105
E
O
HOH
1_555
176.2
A
HOH
101
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
106
E
O
HOH
1_555
86.1
A
HOH
102
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
106
E
O
HOH
1_555
96.1
A
HOH
103
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
106
E
O
HOH
1_555
177.4
A
HOH
104
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
106
E
O
HOH
1_555
88.1
A
HOH
105
E
O
HOH
1_555
A
MG
100
C
MG
MG
1_555
A
HOH
106
E
O
HOH
1_555
90.8
A
HOH
201
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
202
E
O
HOH
1_555
179.4
A
HOH
201
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
203
E
O
HOH
1_555
89.5
A
HOH
202
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
203
E
O
HOH
1_555
90.0
A
HOH
201
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
204
E
O
HOH
1_555
90.8
A
HOH
202
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
204
E
O
HOH
1_555
88.8
A
HOH
203
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
204
E
O
HOH
1_555
88.5
A
HOH
201
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
89.1
A
HOH
202
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
91.3
A
HOH
203
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
92.6
A
HOH
204
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
178.9
A
HOH
201
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
93.2
A
HOH
202
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
87.2
A
HOH
203
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
176.4
A
HOH
204
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
89.0
A
HOH
205
E
O
HOH
1_555
A
MG
200
D
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
89.9
A
XGR
1
A
XGR
1
DG
A
XCR
2
A
XCR
2
DC
A
XGR
3
A
XGR
3
DG
A
XTR
4
A
XTR
4
DT
A
XGR
6
A
XGR
6
DG
A
XCR
7
A
XCR
7
DC
A
XGR
8
A
XGR
8
DG
A
XGR
9
A
XGR
9
DG
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
MG
200
D
MG
1
A
N1
XGR
9
A
N1
XGR
9
1
Y
1
A
C2
XGR
9
A
C2
XGR
9
1
Y
1
A
N2
XGR
9
A
N2
XGR
9
1
Y
1
A
N3
XGR
9
A
N3
XGR
9
1
Y
1
A
C4
XGR
9
A
C4
XGR
9
1
Y
1
A
C5
XGR
9
A
C5
XGR
9
1
Y
1
A
C6
XGR
9
A
C6
XGR
9
1
Y
1
A
O6
XGR
9
A
O6
XGR
9
1
Y
1
A
N7
XGR
9
A
N7
XGR
9
1
Y
1
A
C8
XGR
9
A
C8
XGR
9
1
Y
1
A
N9
XGR
9
A
N9
XGR
9
1
Y
1
A
C1'
XGR
9
A
C1'
XGR
9
1
Y
1
A
C2'
XGR
9
A
C2'
XGR
9
1
Y
1
A
C3'
XGR
9
A
C3'
XGR
9
1
Y
1
A
O3'
XGR
9
A
O3'
XGR
9
1
Y
1
A
C4'
XGR
9
A
C4'
XGR
9
1
Y
1
A
C5'
XGR
9
A
C5'
XGR
9
1
Y
1
A
C6'
XGR
9
A
C6'
XGR
9
1
Y
1
A
C7'
XGR
9
A
C7'
XGR
9
1
Y
1
B
B
C5'
C4'
U
U
4
4
-0.043
0.007
1.508
1.465
N
83.75
61.046
37.01
4.490
2.240
0.000
4.490
0.000
-6.730
0.970
0.958
The Friedel pairs were used in phasing
0.232
0.184
0.187
2.50
36.3
114
2574
4.400
98.020
0.232
0.184
1.00
0.50
0.762
9.838
0.190
0.310
0.237
RANDOM
1
THROUGHOUT
0.00
MOLECULAR REPLACEMENT
0.310
0.237
0.800
0.800
1.400
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.50
36.3
47
390
2
341
0
0.018
0.021
396
2.247
2.972
617
0.120
0.200
63
0.010
0.017
199
0.108
1.500
1
2.812
3.000
392
4.317
4.500
605
0.733
0.379
2.57
9
169
178
20
97.270
2.50
36.3
3KNC
2460
2575
0.048
1
9.400
98.800
data reduction
Andrew G.W. Leslie
andrew@mrc-lmb.cam.ac.uk
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/
MOSFLM
package
data scaling
Phil R. Evans
pre@mrc-lmb.cam.ac.uk
2008/10/21
Fortran_77
http://www.ccp4.ac.uk/dist/html/scala.html
SCALA
other
3.3.9
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Thu Nov 13 11:40:59 2008
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
2.1.4
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.005
data collection
MAR345
CCD
Crystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(CGCUACGC)
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
Biological unit is the same as asymmetric unit
covale
1.572
both
A
XTR
4
A
O3'
XTR
4
1_555
A
XAR
5
A
P
XAR
5
1_555
metalc
2.136
A
MG
100
C
MG
MG
1_555
A
HOH
101
E
O
HOH
1_555
metalc
2.134
A
MG
100
C
MG
MG
1_555
A
HOH
102
E
O
HOH
1_555
metalc
2.130
A
MG
100
C
MG
MG
1_555
A
HOH
103
E
O
HOH
1_555
metalc
2.146
A
MG
100
C
MG
MG
1_555
A
HOH
104
E
O
HOH
1_555
metalc
2.137
A
MG
100
C
MG
MG
1_555
A
HOH
105
E
O
HOH
1_555
metalc
2.141
A
MG
100
C
MG
MG
1_555
A
HOH
106
E
O
HOH
1_555
metalc
2.160
A
MG
200
D
MG
MG
1_555
A
HOH
201
E
O
HOH
1_555
metalc
2.172
A
MG
200
D
MG
MG
1_555
A
HOH
202
E
O
HOH
1_555
metalc
2.176
A
MG
200
D
MG
MG
1_555
A
HOH
203
E
O
HOH
1_555
metalc
2.160
A
MG
200
D
MG
MG
1_555
A
HOH
204
E
O
HOH
1_555
metalc
2.164
A
MG
200
D
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
metalc
2.163
A
MG
200
D
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
hydrog
WATSON-CRICK
A
XGR
1
A
N1
XGR
1
1_555
B
C
8
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
XGR
1
A
N2
XGR
1
1_555
B
C
8
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
XGR
1
A
O6
XGR
1
1_555
B
C
8
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
XCR
2
A
N3
XCR
2
1_555
B
G
7
B
N1
G
7
1_555
hydrog
WATSON-CRICK
A
XCR
2
A
N4
XCR
2
1_555
B
G
7
B
O6
G
7
1_555
hydrog
WATSON-CRICK
A
XCR
2
A
O2
XCR
2
1_555
B
G
7
B
N2
G
7
1_555
hydrog
WATSON-CRICK
A
XGR
3
A
N1
XGR
3
1_555
B
C
6
B
N3
C
6
1_555
hydrog
WATSON-CRICK
A
XGR
3
A
N2
XGR
3
1_555
B
C
6
B
O2
C
6
1_555
hydrog
WATSON-CRICK
A
XGR
3
A
O6
XGR
3
1_555
B
C
6
B
N4
C
6
1_555
hydrog
WATSON-CRICK
A
XTR
4
A
N3
XTR
4
1_555
B
A
5
B
N1
A
5
1_555
hydrog
WATSON-CRICK
A
XTR
4
A
O4
XTR
4
1_555
B
A
5
B
N6
A
5
1_555
hydrog
WATSON-CRICK
A
XGR
6
A
N1
XGR
6
1_555
B
C
3
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
XGR
6
A
N2
XGR
6
1_555
B
C
3
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
XGR
6
A
O6
XGR
6
1_555
B
C
3
B
N4
C
3
1_555
hydrog
WATSON-CRICK
A
XCR
7
A
N3
XCR
7
1_555
B
G
2
B
N1
G
2
1_555
hydrog
WATSON-CRICK
A
XCR
7
A
N4
XCR
7
1_555
B
G
2
B
O6
G
2
1_555
hydrog
WATSON-CRICK
A
XCR
7
A
O2
XCR
7
1_555
B
G
2
B
N2
G
2
1_555
hydrog
WATSON-CRICK
A
XGR
8
A
N1
XGR
8
1_555
B
C
1
B
N3
C
1
1_555
hydrog
WATSON-CRICK
A
XGR
8
A
N2
XGR
8
1_555
B
C
1
B
O2
C
1
1_555
hydrog
WATSON-CRICK
A
XGR
8
A
O6
XGR
8
1_555
B
C
1
B
N4
C
1
1_555
RNA/CYCLOHEXENE-RNA HYBRID
cyclohexene, sugar modification, RNA, RNA-CYCLOHEXENE-RNA HYBRID complex
3KNC
PDB
1
1
3KNC
GCGTAGCGG
3KNC
PDB
2
1
3KNC
CGCUACGC
1
9
3KNC
1
9
3KNC
A
1
1
9
1
8
3KNC
1
8
3KNC
B
2
1
8
1
C
engineered mutation
XGR
1
3KNC
A
3KNC
PDB
2
1
1
G
engineered mutation
XCR
2
3KNC
A
3KNC
PDB
3
2
1
DT
engineered mutation
XGR
3
3KNC
A
3KNC
PDB
4
3
1
A
engineered mutation
XTR
4
3KNC
A
3KNC
PDB
5
4
1
G
engineered mutation
XAR
5
3KNC
A
3KNC
PDB
6
5
1
C
engineered mutation
XGR
6
3KNC
A
3KNC
PDB
7
6
1
G
engineered mutation
XCR
7
3KNC
A
3KNC
PDB
8
7
1
G
engineered mutation
XGR
8
3KNC
A
3KNC
PDB
9
8
1
G
engineered mutation
XGR
9
3KNC
A
3KNC
PDB
10
9
BINDING SITE FOR RESIDUE MG A 100
A
MG
100
Software
6
BINDING SITE FOR RESIDUE MG A 200
A
MG
200
Software
12
A
HOH
101
E
HOH
6
1_555
A
HOH
102
E
HOH
6
1_555
A
HOH
103
E
HOH
6
1_555
A
HOH
104
E
HOH
6
1_555
A
HOH
105
E
HOH
6
1_555
A
HOH
106
E
HOH
6
1_555
A
HOH
201
E
HOH
12
1_555
A
HOH
201
E
HOH
12
5_555
A
HOH
202
E
HOH
12
1_555
A
HOH
202
E
HOH
12
5_555
A
HOH
203
E
HOH
12
1_555
A
HOH
203
E
HOH
12
5_555
A
HOH
204
E
HOH
12
5_555
A
HOH
204
E
HOH
12
1_555
A
HOH
205
E
HOH
12
5_555
A
HOH
205
E
HOH
12
1_555
A
HOH
206
E
HOH
12
5_555
A
HOH
206
E
HOH
12
1_555
154
P 32 2 1