Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54178 Å / Relative weight: 1
Reflection
Resolution: 2.28→42.33 Å / Num. obs: 5759 / % possible obs: 98.4 % / Redundancy: 2.7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.27 / Net I/σ(I): 26.4
Reflection shell
Resolution: 2.28→42.33 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 13.8 / Num. unique obs: 1993 / CC1/2: 0.943 / % possible all: 99.6
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.0258
refinement
XDS
datareduction
Aimless
datascaling
Refinement
Method to determine structure: FOURIER SYNTHESIS Starting model: in house structure Resolution: 2.282→42.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.886 / SU B: 11.117 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.414 / ESU R Free: 0.255 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2339
258
4.565 %
Rwork
0.1393
5394
-
all
0.143
-
-
obs
-
5652
96.106 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parameters
Biso mean: 23.693 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.042 Å2
0 Å2
-0 Å2
2-
-
-0.023 Å2
0 Å2
3-
-
-
-0.019 Å2
Refinement step
Cycle: LAST / Resolution: 2.282→42.33 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
928
0
46
166
1140
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.013
1027
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
950
X-RAY DIFFRACTION
r_angle_refined_deg
1.475
1.677
1379
X-RAY DIFFRACTION
r_angle_other_deg
1.243
1.622
2206
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.56
5
118
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.606
21.607
56
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.986
15
179
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.525
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.071
0.2
118
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1133
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
228
X-RAY DIFFRACTION
r_nbd_refined
0.195
0.2
220
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.175
0.2
788
X-RAY DIFFRACTION
r_nbtor_refined
0.168
0.2
490
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.082
0.2
391
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.197
0.2
88
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.145
0.2
8
X-RAY DIFFRACTION
r_nbd_other
0.185
0.2
48
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.272
0.2
17
X-RAY DIFFRACTION
r_mcbond_it
1.946
2.55
466
X-RAY DIFFRACTION
r_mcbond_other
1.909
2.539
465
X-RAY DIFFRACTION
r_mcangle_it
3.183
5.694
586
X-RAY DIFFRACTION
r_mcangle_other
3.181
5.711
587
X-RAY DIFFRACTION
r_scbond_it
2.609
3.054
561
X-RAY DIFFRACTION
r_scbond_other
2.607
3.056
562
X-RAY DIFFRACTION
r_scangle_it
4.296
6.514
790
X-RAY DIFFRACTION
r_scangle_other
4.293
6.518
791
X-RAY DIFFRACTION
r_lrange_it
7.019
24.01
1238
X-RAY DIFFRACTION
r_lrange_other
7.016
24.027
1239
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.282-2.341
0.218
24
0.138
382
X-RAY DIFFRACTION
98.0676
2.341-2.405
0.393
21
0.14
383
X-RAY DIFFRACTION
98.2968
2.405-2.475
0.199
18
0.136
378
X-RAY DIFFRACTION
97.2973
2.475-2.551
0.22
14
0.126
358
X-RAY DIFFRACTION
97.8947
2.551-2.634
0.236
13
0.119
365
X-RAY DIFFRACTION
98.1818
2.634-2.726
0.146
14
0.1
337
X-RAY DIFFRACTION
96.9613
2.726-2.828
0.29
18
0.11
325
X-RAY DIFFRACTION
98.2808
2.828-2.943
0.122
21
0.123
320
X-RAY DIFFRACTION
96.3277
2.943-3.074
0.225
16
0.13
313
X-RAY DIFFRACTION
98.503
3.074-3.223
0.339
6
0.144
296
X-RAY DIFFRACTION
96.1783
3.223-3.396
0.178
13
0.131
276
X-RAY DIFFRACTION
96.6555
3.396-3.601
0.248
12
0.141
271
X-RAY DIFFRACTION
96.2585
3.601-3.847
0.241
8
0.128
251
X-RAY DIFFRACTION
97.0037
3.847-4.153
0.448
12
0.134
233
X-RAY DIFFRACTION
96.4567
4.153-4.544
0.17
7
0.14
230
X-RAY DIFFRACTION
98.3402
4.544-5.074
0.229
12
0.154
199
X-RAY DIFFRACTION
97.235
5.074-5.845
0.228
12
0.192
168
X-RAY DIFFRACTION
92.7835
5.845-7.124
0.471
8
0.204
138
X-RAY DIFFRACTION
86.9048
7.124-9.935
0.172
5
0.126
116
X-RAY DIFFRACTION
82.8767
9.935-42.332
0.264
4
0.249
55
X-RAY DIFFRACTION
64.8352
Refinement TLS params.
Method: refined / Origin x: 32.9643 Å / Origin y: 10.0222 Å / Origin z: 0.5811 Å
11
12
13
21
22
23
31
32
33
T
0.013 Å2
-0.0002 Å2
-0.0037 Å2
-
0.0104 Å2
0.0047 Å2
-
-
0.0089 Å2
L
0.7733 °2
0.0974 °2
0.2757 °2
-
0.2659 °2
0.0534 °2
-
-
0.1036 °2
S
0.0379 Å °
0.0197 Å °
0.0457 Å °
0.0041 Å °
-0.0479 Å °
-0.011 Å °
0.0202 Å °
0.0028 Å °
0.01 Å °
Refinement TLS group
Selection: ALL
+
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