BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Resolution: 1.85→29.025 Å / Num. obs: 14324 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 5.3
Reflection shell
Rmerge(I) obs: 0.016 / Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.85-1.9
8.8
0.5
8996
1026
0.01628
99.8
1.9-1.95
8.7
0.6
8720
1001
0.01231
99.9
1.95-2.01
8.7
0.9
8398
965
0.876
99.9
2.01-2.07
8.7
1.1
8307
954
0.672
99.9
2.07-2.14
8.7
1.5
7902
913
0.517
100
2.14-2.21
8.7
2
7757
895
0.386
100
2.21-2.29
8.6
2.4
7463
866
0.318
100
2.29-2.39
8.6
2.7
7086
828
0.286
100
2.39-2.49
8.6
3.1
6902
807
0.244
100
2.49-2.62
8.4
3.6
6598
783
0.211
100
2.62-2.76
8.4
4.9
6164
731
0.155
100
2.76-2.93
8.4
6.2
5847
698
0.121
100
2.93-3.13
8.3
7.6
5574
673
0.098
100
3.13-3.38
8.2
10.5
5023
615
0.069
100
3.38-3.7
8.1
11.3
4754
587
0.061
100
3.7-4.14
7.8
12.9
4152
533
0.05
100
4.14-4.78
7.3
13.8
3467
478
0.044
100
4.78-5.85
7.5
14.2
3117
413
0.044
100
5.85-8.27
7.5
14.7
2580
343
0.044
100
8.27-29.03
6.4
13.2
1368
215
0.039
98
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SHELX
phasing
REFMAC
5.2.0019
refinement
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SHELXD
phasing
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.85→29.025 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.788 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL SE-MET INCORPORATION. (3) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.225
718
5 %
RANDOM
Rwork
0.192
-
-
-
obs
0.193
14279
99.88 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 20.411 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.78 Å2
0.39 Å2
0 Å2
2-
-
0.78 Å2
0 Å2
3-
-
-
-1.17 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→29.025 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
922
0
0
76
998
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
971
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
643
X-RAY DIFFRACTION
r_angle_refined_deg
1.555
1.937
1325
X-RAY DIFFRACTION
r_angle_other_deg
1.001
3
1562
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.051
5
117
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.037
23.8
50
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.245
15
164
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.939
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.103
0.2
147
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1095
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
210
X-RAY DIFFRACTION
r_nbd_refined
0.208
0.2
168
X-RAY DIFFRACTION
r_nbd_other
0.197
0.2
688
X-RAY DIFFRACTION
r_nbtor_refined
0.183
0.2
464
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
523
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.161
0.2
59
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.119
0.2
11
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.286
0.2
24
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.175
0.2
11
X-RAY DIFFRACTION
r_mcbond_it
2.546
3
635
X-RAY DIFFRACTION
r_mcbond_other
0.599
3
229
X-RAY DIFFRACTION
r_mcangle_it
3.582
5
945
X-RAY DIFFRACTION
r_scbond_it
5.931
8
440
X-RAY DIFFRACTION
r_scangle_it
7.958
11
380
LS refinement shell
Resolution: 1.85→1.898 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.396
50
-
Rwork
0.287
973
-
obs
-
1023
99.71 %
Refinement TLS params.
Method: refined / Origin x: 14.4618 Å / Origin y: 17.0405 Å / Origin z: -4.1336 Å
11
12
13
21
22
23
31
32
33
T
-0.0277 Å2
0.0148 Å2
0.0015 Å2
-
-0.0391 Å2
-0.0151 Å2
-
-
-0.0307 Å2
L
0.7855 °2
0.1159 °2
0.3207 °2
-
0.7617 °2
-0.3568 °2
-
-
2.1897 °2
S
-0.0282 Å °
-0.0518 Å °
0.0687 Å °
0.1022 Å °
-0.0344 Å °
-0.0192 Å °
-0.1819 Å °
-0.234 Å °
0.0625 Å °
Refinement TLS group
Selection: ALL
+
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