BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.53 Å3/Da / Density % sol: 65.11 % Description: THE EXPERIMENTAL MAD MAP WAS PARTIALLY AUTOTRACED WITH RESOLVE. TO AID IN COMPLETING THE TRACE, A MOLECULAR REPLACEMENT SOLUTION (USING 1G59 CHAIN-A AS A SEARCH MODEL) THAT HAD BEEN ...Description: THE EXPERIMENTAL MAD MAP WAS PARTIALLY AUTOTRACED WITH RESOLVE. TO AID IN COMPLETING THE TRACE, A MOLECULAR REPLACEMENT SOLUTION (USING 1G59 CHAIN-A AS A SEARCH MODEL) THAT HAD BEEN PARTIALLY REFINED AGAINST A LOWER RESOLUTION TM1351 DATA SET WAS SUPERIMPOSED ON AUTOTRACED MODEL.
Resolution: 2.34→47.351 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 27.009 / SU ML: 0.278 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.247 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GOL MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. UNEXPLAINED DENSITY NEAR A15, A323, AND A432. 6. DUE TO STRONG ICE RINGS 4928 REFLECTIONS BETWEEN 2.732-2.654, 2.584-2.551, AND 2.463-2.411 ANGSTROMS WERE OMITTED FROM THE FINAL REFINEMENT. 7. THE NOMINAL RESOLUTION IS 2.50 A WITH 4299 OBSERVED REFLECTIONS BETWEEN 2.50-2.34 (69.1% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.268
1524
5 %
RANDOM
Rwork
0.234
-
-
-
obs
0.236
30264
85.96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 23.855 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.18 Å2
-0.09 Å2
0 Å2
2-
-
-0.18 Å2
0 Å2
3-
-
-
0.27 Å2
Refinement step
Cycle: LAST / Resolution: 2.34→47.351 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3828
0
9
60
3897
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
3927
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
2833
X-RAY DIFFRACTION
r_angle_refined_deg
1.427
1.983
5293
X-RAY DIFFRACTION
r_angle_other_deg
1.235
3
6859
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.06
5
467
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
27.887
23.298
191
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.179
15
718
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.053
15
33
X-RAY DIFFRACTION
r_chiral_restr
0.083
0.2
558
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
4303
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
833
X-RAY DIFFRACTION
r_nbd_refined
0.144
0.2
717
X-RAY DIFFRACTION
r_nbd_other
0.117
0.2
2728
X-RAY DIFFRACTION
r_nbtor_refined
0.146
0.2
1838
X-RAY DIFFRACTION
r_nbtor_other
0.067
0.2
1795
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.078
0.2
74
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.104
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.111
0.2
34
X-RAY DIFFRACTION
r_mcbond_it
0.347
1.5
2521
X-RAY DIFFRACTION
r_mcbond_other
0.044
1.5
937
X-RAY DIFFRACTION
r_mcangle_it
0.528
2
3781
X-RAY DIFFRACTION
r_scbond_it
0.662
3
1725
X-RAY DIFFRACTION
r_scangle_it
0.998
4.5
1512
LS refinement shell
Resolution: 2.34→2.401 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.391
129
-
Rwork
0.404
2431
-
obs
-
2560
99.92 %
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
2.0815
-0.8882
0.0073
1.9659
0.1736
4.1959
0.0288
0.2538
0.1672
-0.1355
-0.0336
-0.0268
0.1633
0.1744
0.0048
0.6862
0.2821
-0.1361
0.2733
-0.0828
0.1222
-43.074
12.47
39.495
2
3.205
1.862
3.7834
1.2002
2.1741
5.9364
0.3974
0.3872
-0.1142
0.0575
0.0133
-0.2789
-0.0715
0.997
-0.4107
0.7352
0.1762
-0.0815
0.6777
-0.1432
0.3207
-23.236
25.07
82.786
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
ID
Refine TLS-ID
Auth seq-ID
Label seq-ID
1
1
1 - 251
13 - 263
2
2
252 - 468
264 - 480
+
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