Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN A, TYR 161 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN A, TYR 161 TO GLU ENGINEERED RESIDUE IN CHAIN B, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN B, TYR 161 TO GLU ENGINEERED RESIDUE IN CHAIN C, THR 159 TO ASP ENGINEERED RESIDUE IN CHAIN C, TYR 161 TO GLU
Sequence details
CONFLICT Q274E IS A DOCUMENTED NATURAL VARIANT. CONFLICT A152 AND N301D ARE DOCUMENTED SEQUENCE ...CONFLICT Q274E IS A DOCUMENTED NATURAL VARIANT. CONFLICT A152 AND N301D ARE DOCUMENTED SEQUENCE CONFLICTS. CONTAINS TWO PHOSPHO-MIMETIC ACTIVATING MUTATIONS, Y161E AND T159D.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.08 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal grow
Details: 17.5% PEG 3350, 0.1 M (NH4)CL PH 6.3, 0.05 M MG FORMATE
Resolution: 2.4→29.78 Å / Cor.coef. Fo:Fc: 0.9582 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.479 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.446 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.245 Details: RESIDUES 152-163 OF CHAIN A AND RESIDUE 39-40 OF CHAIN B ARE DISORDERED. IDEAL-DIST CONTACT TERM SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. NCS REPRESENTATION IS RESTRAINT LSSR (- ...Details: RESIDUES 152-163 OF CHAIN A AND RESIDUE 39-40 OF CHAIN B ARE DISORDERED. IDEAL-DIST CONTACT TERM SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. NCS REPRESENTATION IS RESTRAINT LSSR (-AUTONCS). NUMBER OF RESTRAIN LIBRARIES USED 9.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2261
1676
5.06 %
RANDOM
Rwork
0.1865
-
-
-
obs
0.1885
33152
99.98 %
-
Displacement parameters
Biso mean: 60.66 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.823 Å2
0 Å2
0 Å2
2-
-
1.823 Å2
0 Å2
3-
-
-
-3.6459 Å2
Refine analyze
Luzzati coordinate error obs: 0.305 Å
Refinement step
Cycle: LAST / Resolution: 2.4→29.78 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6399
0
96
315
6810
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
6673
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.03
9093
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2983
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
115
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
984
HARMONIC
5
X-RAY DIFFRACTION
t_it
6673
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.69
X-RAY DIFFRACTION
t_other_torsion
2.68
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
869
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
7634
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.4→2.47 Å / Total num. of bins used: 17
Rfactor
Num. reflection
% reflection
Rfree
0.2461
127
4.35 %
Rwork
0.2
2792
-
all
0.202
2919
-
obs
-
-
99.98 %
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
2.2045
0.6197
-0.0418
4.1265
0.9606
1.8869
-0.2934
-0.083
-0.0202
-0.0417
0.0457
0.4366
0.0572
-0.3378
0.2477
-0.1903
-0.0097
0.0115
-0.1486
-0.0473
-0.1162
42.4489
102.6769
-1.5262
2
5.3932
0.3891
-0.8314
1.7727
-0.0315
1.1488
-0.1981
0.1849
-0.3674
0.2056
0.0127
-0.1001
0.3243
0.2597
0.1854
-0.1749
0.0714
0.0761
-0.1899
0.0248
-0.103
14.5105
129.448
3.2681
3
3.8505
-1.3469
1.7594
2.8641
-0.8628
2.214
-0.0167
0.0082
0.527
0.0398
0.0235
-0.1805
-0.2978
0.0891
-0.0069
-0.1531
-0.0125
0.0753
-0.1926
0.0248
-0.0912
5.2043
90.8823
-6.348
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
3
X-RAY DIFFRACTION
3
CHAINC
+
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