Resolution: 1.66→28.75 Å / Num. obs: 62701 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 33.53 Å2 / Rsym value: 0.099 / Net I/σ(I): 13
Reflection shell
Resolution: 1.66→1.75 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 8969 / Rsym value: 0.553 / % possible all: 98.5
-
Processing
Software
Name
Version
Classification
XDS
datascaling
SCALA
5.0)
datascaling
SHELX
SHARP/autoSHARP
modelbuilding
REFMAC
5.2.0005
refinement
XDS
datareduction
CCP4
(SCALA)
datascaling
SHELX
phasing
SHARP
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.66→28.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.078 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.086 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITIES FOR LOOPS 70-72 FOR CHAIN A, B AND C ARE AMBIGUOUS. 3. THE BIOLOGICAL UNIT IS LIKELY A HEXAMER WITH D3 SYMMETRY. WITHIN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITIES FOR LOOPS 70-72 FOR CHAIN A, B AND C ARE AMBIGUOUS. 3. THE BIOLOGICAL UNIT IS LIKELY A HEXAMER WITH D3 SYMMETRY. WITHIN THE HEXAMER, THERE ARE THREE DIMERS WITH A LARGE INTERACTION SURFACE. THESE DIMERS ARE FORMED FROM THE THREE MONOMERS IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT AND CRYSTALLOGRAPHIC SYMMETRY. THESE PAIRS ARE A:A' (8_565), B:C, AND B' (8_565):C' (8_565). THE COA BINDS AT THE INTERFACE BETWEEN THE DIMERS. FOR THE B:C DIMERS, ONLY ONE BINDING SITE IS OCCUPIED. A PHOSPHATE IS VISIBLE IN THE NON-CRYSTALLOGRAPHIC SYMMETRY COA BINDING SITE. THIS PHOSPHATE COULD BE FROM BUFFER OR PRODUCED BY HYDROLYSIS OF COA. THIS SECOND SITE IS PARTIALLY OCCLUDED BY THE PACKING OF HEXAMERS IN THE UNIT CELL. 4. THERE IS SOME EXTRA DENSITY NEAR CHAIN B/SER 10. IT WAS MODELED AS A CLOSE CONTACT WATER.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19669
3188
5.1 %
RANDOM
Rwork
0.17012
-
-
-
obs
0.17146
59512
99.36 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 26.825 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.4 Å2
0 Å2
0 Å2
2-
-
-0.37 Å2
0 Å2
3-
-
-
-2.03 Å2
Refinement step
Cycle: LAST / Resolution: 1.66→28.75 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3481
0
101
310
3892
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
3703
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3396
X-RAY DIFFRACTION
r_angle_refined_deg
1.728
1.995
5061
X-RAY DIFFRACTION
r_angle_other_deg
0.887
3
7871
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.613
5
461
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.085
23.581
148
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.879
15
603
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.924
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.102
0.2
610
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
4016
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
687
X-RAY DIFFRACTION
r_nbd_refined
0.213
0.2
699
X-RAY DIFFRACTION
r_nbd_other
0.192
0.2
3394
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
2358
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.209
0.2
259
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.084
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.213
0.2
88
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.189
0.2
22
X-RAY DIFFRACTION
r_mcbond_it
2.635
3
2493
X-RAY DIFFRACTION
r_mcbond_other
0.691
3
933
X-RAY DIFFRACTION
r_mcangle_it
3.274
5
3799
X-RAY DIFFRACTION
r_scbond_it
5.79
8
1447
X-RAY DIFFRACTION
r_scangle_it
7.504
11
1262
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.2
1813
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.07
0.2
1
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
476
mediumpositional
0.21
0.5
2
B
476
mediumpositional
0.13
0.5
3
C
476
mediumpositional
0.2
0.5
1
A
602
loosepositional
0.57
5
2
B
602
loosepositional
0.41
5
3
C
602
loosepositional
0.46
5
1
A
476
mediumthermal
1.04
2
2
B
476
mediumthermal
1.27
2
3
C
476
mediumthermal
1.18
2
1
A
602
loosethermal
2.31
10
2
B
602
loosethermal
2.91
10
3
C
602
loosethermal
2.4
10
LS refinement shell
Resolution: 1.66→1.703 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.292
222
4.95 %
Rwork
0.255
4262
-
obs
-
-
97.04 %
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
0.9746
-0.1205
-0.0596
0.683
0.0795
0.9576
0.0052
-0.0626
-0.0202
0.0425
-0.0016
0.031
0.0982
-0.0527
-0.0036
-0.1079
-0.0124
0.007
-0.0627
-0.0083
-0.0415
-2.7579
57.9125
39.8724
2
0.8354
-0.5183
0.7796
2.1313
-1.3517
6.9206
-0.0015
-0.0155
0.0649
-0.2101
0.0012
-0.1252
0.2081
0.1254
0.0003
-0.1185
0.0082
0.0073
0.024
-0.0388
-0.0283
37.5437
59.1564
40.7104
3
0.9125
-0.4696
0.4098
1.608
-0.2579
1.3223
0.0658
0.1022
0.0358
0.0056
-0.0348
-0.0486
0.0933
0.1306
-0.031
-0.1366
0.0293
-0.0165
0.0153
-0.0088
-0.0406
18.5244
70.7344
44.6522
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
2 - 156
14 - 168
2
2
B
B
3 - 153
15 - 165
3
3
C
C
0 - 153
12 - 165
+
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