Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore central transport channel / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / mRNA transport / protein import into nucleus / RNA binding / nucleus Similarity search - Function
Nuclear RNA export factor / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Leucine-rich repeat domain superfamily / Roll / Alpha Beta Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH - SAD / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979 Å / Relative weight: 1
Reflection
Resolution: 1.84→50 Å / Num. obs: 27423 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.068 / Rsym value: 0.05 / Net I/σ(I): 13.3
Reflection shell
Resolution: 1.84→1.87 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.327 / % possible all: 98.1
-
Processing
Software
Name
Version
Classification
AutoSol
(PHENIX.AUTOSOL)
phasing
PHENIX
(PHENIX.REFINE)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.84→47.01 Å / SU ML: 0.21 / σ(F): 1.35 / Stereochemistry target values: MLHL Details: THE CLOSE CONTACTS ARE AT SURFACE AND ARE LIKELY DUE TO CRYSTAL PACKING. ALA 290 AND ARG 368 ARE IN GOOD DENSITY AND PART OF WELL-RESOLVED IRREGULAR LOOPS
Rfactor
Num. reflection
% reflection
Rfree
0.191
1381
5.05 %
Rwork
0.166
-
-
obs
0.167
27364
98.8 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.42 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Biso mean: 23.75 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.448 Å2
0 Å2
-0 Å2
2-
-
1.415 Å2
0 Å2
3-
-
-
-0.966 Å2
Refinement step
Cycle: LAST / Resolution: 1.84→47.01 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2660
0
62
292
3014
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.023
2862
X-RAY DIFFRACTION
f_angle_d
1.585
3880
X-RAY DIFFRACTION
f_dihedral_angle_d
19.532
1089
X-RAY DIFFRACTION
f_chiral_restr
0.124
426
X-RAY DIFFRACTION
f_plane_restr
0.008
503
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.84-1.908
0.259
122
0.193
2480
X-RAY DIFFRACTION
95
1.908-1.984
0.249
141
0.179
2501
X-RAY DIFFRACTION
98
1.984-2.075
0.203
123
0.164
2537
X-RAY DIFFRACTION
98
2.075-2.184
0.192
115
0.157
2587
X-RAY DIFFRACTION
99
2.184-2.321
0.21
144
0.155
2592
X-RAY DIFFRACTION
99
2.321-2.5
0.195
159
0.168
2583
X-RAY DIFFRACTION
99
2.5-2.752
0.2
163
0.165
2575
X-RAY DIFFRACTION
100
2.752-3.15
0.166
117
0.164
2650
X-RAY DIFFRACTION
100
3.15-3.968
0.15
146
0.142
2668
X-RAY DIFFRACTION
100
3.968-47.021
0.173
151
0.167
2810
X-RAY DIFFRACTION
100
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
0.7031
0.0622
-0.1121
1.0469
0.1254
1.2388
0.004
0.0992
0.0596
0.0177
-0.0029
0.074
-0.1431
0.0106
-0.0073
0.0371
0.0083
0.0082
0.0392
0.0185
0.0639
35.3942
39.8125
52.1099
2
0.5638
0.1166
0.0496
0.6715
-0.2647
0.6405
0.031
0.018
-0.1531
0.1044
-0.0064
0.0317
0.1261
-0.004
-0.0245
0.0989
0.0054
0.0119
0.0555
-0.0017
0.1178
35.3877
21.9268
60.4782
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
+
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