Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54178 Å / Relative weight: 1
Reflection
Resolution: 1.55→42.38 Å / Num. obs: 16200 / % possible obs: 89.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 31.6
Reflection shell
Resolution: 1.55→1.64 Å / Redundancy: 2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1479 / % possible all: 52.5
-
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 model Resolution: 1.55→42.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.406 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.091 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1947
769
4.768 %
Rwork
0.1648
15359
-
all
0.166
-
-
obs
-
16128
88.223 %
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: 19.837 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.008 Å2
-0 Å2
-0 Å2
2-
-
-0.004 Å2
0 Å2
3-
-
-
0.012 Å2
Refinement step
Cycle: LAST / Resolution: 1.55→42.38 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
926
0
56
228
1210
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.003
0.013
1036
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
958
X-RAY DIFFRACTION
r_angle_refined_deg
1.163
1.659
1391
X-RAY DIFFRACTION
r_angle_other_deg
1.245
1.625
2227
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.646
5
118
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.594
21.607
56
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.856
15
177
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.771
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.06
0.2
122
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1130
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
227
X-RAY DIFFRACTION
r_nbd_refined
0.194
0.2
217
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.166
0.2
831
X-RAY DIFFRACTION
r_nbtor_refined
0.167
0.2
491
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.078
0.2
373
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.095
0.2
156
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.003
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.136
0.2
13
X-RAY DIFFRACTION
r_nbd_other
0.143
0.2
54
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.091
0.2
38
X-RAY DIFFRACTION
r_mcbond_it
1.169
2.292
466
X-RAY DIFFRACTION
r_mcbond_other
1.145
2.282
465
X-RAY DIFFRACTION
r_mcangle_it
2.037
5.122
586
X-RAY DIFFRACTION
r_mcangle_other
2.04
5.136
587
X-RAY DIFFRACTION
r_scbond_it
1.453
2.592
570
X-RAY DIFFRACTION
r_scbond_other
1.451
2.592
571
X-RAY DIFFRACTION
r_scangle_it
2.462
5.578
802
X-RAY DIFFRACTION
r_scangle_other
2.461
5.579
803
X-RAY DIFFRACTION
r_lrange_it
5.921
23.535
1294
X-RAY DIFFRACTION
r_lrange_other
5.919
23.528
1295
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
1.549-1.589
0.232
24
0.256
539
0.255
1317
0.892
0.908
42.7487
0.222
1.589-1.633
0.194
30
0.217
693
0.216
1285
0.928
0.917
56.2646
0.183
1.633-1.68
0.25
38
0.209
879
0.21
1264
0.899
0.925
72.5475
0.168
1.68-1.732
0.169
47
0.175
1019
0.175
1200
0.951
0.954
88.8333
0.147
1.732-1.789
0.239
59
0.188
1085
0.19
1211
0.938
0.95
94.4674
0.158
1.789-1.851
0.177
57
0.169
1051
0.169
1141
0.953
0.957
97.1078
0.144
1.851-1.921
0.205
65
0.169
1018
0.171
1116
0.949
0.961
97.043
0.148
1.921-1.999
0.194
49
0.159
1002
0.16
1073
0.966
0.972
97.9497
0.142
1.999-2.088
0.15
38
0.163
942
0.162
1011
0.976
0.972
96.9337
0.15
2.088-2.19
0.152
34
0.157
947
0.157
1004
0.972
0.973
97.7092
0.14
2.19-2.308
0.169
41
0.148
890
0.148
946
0.964
0.973
98.4144
0.131
2.308-2.447
0.175
43
0.149
841
0.15
899
0.961
0.971
98.3315
0.135
2.447-2.616
0.202
38
0.15
795
0.152
841
0.96
0.97
99.0488
0.136
2.616-2.824
0.165
35
0.151
731
0.152
778
0.968
0.966
98.4576
0.138
2.824-3.092
0.175
51
0.153
678
0.154
736
0.963
0.967
99.0489
0.146
3.092-3.455
0.188
31
0.165
635
0.166
674
0.961
0.965
98.8131
0.159
3.455-3.985
0.242
31
0.162
555
0.166
599
0.939
0.965
97.8297
0.165
3.985-4.87
0.221
24
0.15
465
0.154
511
0.958
0.969
95.6947
0.168
4.87-6.842
0.272
22
0.184
383
0.188
417
0.942
0.962
97.1223
0.203
6.842-42.381
0.184
12
0.207
211
0.205
255
0.973
0.956
87.451
0.225
+
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