Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.75 Å3/Da / Density % sol: 55.29 % / Description: plates
Crystal grow
Temperature: 282.15 K / Method: vapor diffusion, sitting drop Details: 18% (w/v) PEG 3350, 100 mM Bis tris propane/ hydrochloric acid pH 7.5, 200 mM sodium fluoride, and 3% 2-propanol
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Resolution: 2.52→2.528 Å / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 698 / CC1/2: 0.829
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0267
refinement
autoPROC
datareduction
autoPROC
datascaling
CRANK2
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→115.115 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.409 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.578 / ESU R Free: 0.297 / Details: Hydrogens have not been used
Rfactor
Num. reflection
% reflection
Rfree
0.2503
3422
4.967 %
Rwork
0.1892
65477
-
all
0.192
-
-
obs
-
68899
98.889 %
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: 87.984 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.056 Å2
0 Å2
-1.312 Å2
2-
-
3.1 Å2
-0 Å2
3-
-
-
-5.293 Å2
Refinement step
Cycle: LAST / Resolution: 2.52→115.115 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
13522
0
0
384
13906
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.012
13787
X-RAY DIFFRACTION
r_angle_refined_deg
1.239
1.626
18601
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.092
5
1668
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.94
23.814
721
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.603
15
2554
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.298
15
59
X-RAY DIFFRACTION
r_chiral_restr
0.109
0.2
1758
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
10289
X-RAY DIFFRACTION
r_nbd_refined
0.224
0.2
6664
X-RAY DIFFRACTION
r_nbtor_refined
0.312
0.2
9533
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.202
0.2
662
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.226
0.2
41
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.124
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
6.131
8.668
6693
X-RAY DIFFRACTION
r_mcangle_it
9.332
12.982
8354
X-RAY DIFFRACTION
r_scbond_it
6.66
9.003
7094
X-RAY DIFFRACTION
r_scangle_it
9.95
13.358
10247
X-RAY DIFFRACTION
r_lrange_it
14.335
114.649
21504
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.148
0.05
25536
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Refine-ID
Type
Rms dev position (Å)
Weight position
1
1
A
X-RAY DIFFRACTION
Localncs
0.14843
0.05008
1
2
B
X-RAY DIFFRACTION
Localncs
0.14843
0.05008
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
2.52-2.585
0.38
247
0.314
4830
0.317
5103
0.635
0.683
99.4905
0.305
2.585-2.656
0.305
251
0.272
4740
0.274
5022
0.776
0.791
99.3827
0.26
2.656-2.733
0.291
247
0.241
4619
0.244
4906
0.833
0.85
99.1847
0.226
2.733-2.817
0.337
240
0.234
4431
0.239
4713
0.817
0.864
99.1088
0.22
2.817-2.909
0.264
212
0.214
4377
0.216
4627
0.885
0.895
99.1787
0.199
2.909-3.011
0.27
219
0.204
4030
0.208
4401
0.87
0.903
96.5462
0.188
3.011-3.125
0.282
210
0.19
3970
0.194
4306
0.885
0.917
97.0739
0.175
3.125-3.252
0.25
196
0.185
3932
0.188
4151
0.898
0.925
99.4459
0.172
3.252-3.397
0.28
185
0.19
3729
0.194
3936
0.888
0.924
99.4411
0.18
3.397-3.563
0.253
186
0.178
3547
0.182
3753
0.915
0.938
99.4671
0.174
3.563-3.755
0.246
183
0.181
3407
0.184
3616
0.914
0.941
99.281
0.179
3.755-3.983
0.236
170
0.182
3225
0.185
3417
0.929
0.943
99.3562
0.184
3.983-4.257
0.227
142
0.171
3063
0.174
3219
0.936
0.948
99.5651
0.182
4.257-4.598
0.242
144
0.164
2828
0.168
2979
0.931
0.95
99.765
0.179
4.598-5.036
0.249
132
0.163
2592
0.167
2742
0.917
0.947
99.3435
0.183
5.036-5.629
0.214
131
0.185
2286
0.187
2472
0.937
0.94
97.7751
0.206
5.629-6.497
0.26
101
0.209
2003
0.211
2190
0.915
0.932
96.0731
0.233
6.497-7.951
0.208
103
0.182
1767
0.184
1873
0.95
0.95
99.8398
0.216
7.951-11.218
0.182
81
0.151
1359
0.153
1441
0.957
0.965
99.9306
0.192
11.218-115.115
0.358
42
0.236
742
0.242
806
0.875
0.92
97.2705
0.383
+
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