Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54178 Å / Relative weight: 1
Reflection
Resolution: 2.1→41.744 Å / Num. obs: 28728 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.959 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.16
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.1-2.15
0.257
7.5
11208
1974
91.9
2.15-2.21
0.247
9.5
14368
2027
97.4
2.21-2.28
0.241
10.3
13452
1964
97.3
2.28-2.35
0.205
11.2
14212
1936
97.9
2.35-2.42
0.178
12.1
13811
1879
98
2.42-2.51
0.159
13.4
13340
1815
98.4
2.51-2.6
0.147
13.9
12965
1758
98.4
2.6-2.71
0.143
14.7
12275
1701
98.7
2.71-2.83
0.114
16.6
12176
1652
98.9
2.83-2.97
0.09
19.9
11507
1560
99
2.97-3.13
0.069
24.2
10938
1486
99.2
3.13-3.32
0.056
28.8
10552
1429
99.2
3.32-3.55
0.047
38.5
9657
1342
99.3
3.55-3.83
0.042
44.2
8929
1242
99
3.83-4.2
0.034
53.4
8234
1168
99.4
4.2-4.7
0.031
53.8
7676
1054
99.4
4.7-5.42
0.037
45.5
6799
941
99.7
5.42-6.64
0.044
37.4
5733
800
99.6
6.64-9.39
0.032
50.3
4425
633
99.4
9.39
0.02
74.3
2347
367
96.1
-
Phasing
Phasing
Method: molecular replacement
Phasing MR
Model details: Phaser MODE: MR_AUTO
Highest resolution
Lowest resolution
Rotation
2.5 Å
41.78 Å
Translation
2.5 Å
41.78 Å
-
Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
PHASER
phasing
REFMAC
5.6.0117
refinement
PDB_EXTRACT
3.004
dataextraction
XDS
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.744 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.428 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.195
1444
5 %
RANDOM
Rwork
0.158
-
-
-
obs
0.16
28728
98 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 16.846 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.15 Å2
-0 Å2
-0 Å2
2-
-
0.12 Å2
0 Å2
3-
-
-
-0.27 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→41.744 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3499
0
78
416
3993
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.019
3666
X-RAY DIFFRACTION
r_bond_other_d
0.006
0.02
2504
X-RAY DIFFRACTION
r_angle_refined_deg
1.46
1.979
4976
X-RAY DIFFRACTION
r_angle_other_deg
1.146
3
6096
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.808
5
453
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.264
23.725
153
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.972
15
602
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
26.271
15
21
X-RAY DIFFRACTION
r_chiral_restr
0.084
0.2
541
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
4031
X-RAY DIFFRACTION
r_gen_planes_other
0.005
0.02
762
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.23
101
-
Rwork
0.167
1784
-
all
-
1885
-
obs
-
-
91.5 %
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
0.6235
-0.0804
-0.0412
1.0742
-0.1296
0.4986
-0.059
-0.1008
-0.0517
0.0729
0.0381
-0.0584
0.0112
0.0902
0.0209
0.0116
0.0181
0.0012
0.0518
0.0092
0.0235
17.3711
14.0303
37.4601
2
1.1654
0.1881
-0.0104
0.4613
-0.1522
0.6527
-0.0134
0.1689
-0.0364
-0.0728
-0.003
-0.0333
0.0069
0.1191
0.0164
0.029
0.0002
0.0236
0.0753
-0.0139
0.0295
15.4394
17.4776
13.6591
3
0.7841
0.2742
0.126
0.6715
0.1397
0.3702
-0.0081
-0.0412
0.0344
0.0624
0.0072
-0.0175
-0.1344
0.013
0.0009
0.0858
-0.0089
-0.0041
0.0072
-0.0075
0.0165
3.6053
44.3974
39.9069
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 151
2
X-RAY DIFFRACTION
1
A
201 - 202
3
X-RAY DIFFRACTION
2
B
2 - 151
4
X-RAY DIFFRACTION
2
B
201 - 202
5
X-RAY DIFFRACTION
3
C
1 - 152
6
X-RAY DIFFRACTION
3
C
201 - 202
+
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