Resolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3539 / Mean I/σ(I) obs: 4.8 / Num. unique all: 661 / % possible all: 81.4
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0003
refinement
HKL-2000
datacollection
X-GEN
datareduction
X-GEN
datascaling
MOLREP
(CCP4)
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: A cononical A-RNA dodecamer generated with the program TURBO-FRODO omitting U13 and U26. Resolution: 1.8→44.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.576 / SU ML: 0.135 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.21 Stereochemistry target values: Standard Refmac parameters and the parameters generated by PRODRG (Schuettelkopf, A. W. and van Aalten, D.M.F. 2004. PRODRG: a tool for high-throughput crystallography ...Stereochemistry target values: Standard Refmac parameters and the parameters generated by PRODRG (Schuettelkopf, A. W. and van Aalten, D.M.F. 2004. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr. D Biol. Crystallogr. 60: 1355-1363.) for the residue M2G. Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27742
582
10.8 %
RANDOM
Rwork
0.19005
-
-
-
obs
0.19938
4816
84.12 %
-
all
-
6420
-
-
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: 25.807 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.88 Å2
0 Å2
0.63 Å2
2-
-
0.18 Å2
0 Å2
3-
-
-
1.86 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→44.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
556
0
115
671
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.021
620
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
222
X-RAY DIFFRACTION
r_angle_refined_deg
1.356
3.007
948
X-RAY DIFFRACTION
r_angle_other_deg
1.124
3
576
X-RAY DIFFRACTION
r_chiral_restr
0.051
0.2
126
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
276
X-RAY DIFFRACTION
r_gen_planes_other
0.004
0.02
2
X-RAY DIFFRACTION
r_nbd_refined
0.108
0.2
76
X-RAY DIFFRACTION
r_nbd_other
0.249
0.2
276
X-RAY DIFFRACTION
r_nbtor_refined
0.236
0.2
230
X-RAY DIFFRACTION
r_nbtor_other
0.077
0.2
128
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.146
0.2
85
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.075
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.084
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.212
0.2
27
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.154
0.2
28
X-RAY DIFFRACTION
r_scbond_it
1.582
3
931
X-RAY DIFFRACTION
r_scangle_it
1.993
4.5
948
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.248
25
-
Rwork
0.209
235
-
obs
-
235
56.16 %
Refinement TLS params.
Method: refined / Origin x: 0.1389 Å / Origin y: -1.8722 Å / Origin z: 10.7909 Å
11
12
13
21
22
23
31
32
33
T
-0.0232 Å2
0.0022 Å2
0.0009 Å2
-
-0.0549 Å2
-0.0114 Å2
-
-
-0.0589 Å2
L
2.0857 °2
-0.3434 °2
0.2795 °2
-
0.2961 °2
-0.2948 °2
-
-
0.6885 °2
S
-0.0909 Å °
0.0157 Å °
-0.0475 Å °
0.0225 Å °
0.0412 Å °
-0.0166 Å °
-0.0058 Å °
0.0232 Å °
0.0496 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
1 - 13
1 - 13
2
X-RAY DIFFRACTION
1
B
B
14 - 26
1 - 13
+
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