SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: K132Y, K133Y AND K134Y
Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.3 Å3/Da / Density % sol: 46.42 % Description: TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. A 2.30 ANGSTROM MAD DATA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN INITIAL MODEL. THE MODEL WAS THEN REFINED ...Description: TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. A 2.30 ANGSTROM MAD DATA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN INITIAL MODEL. THE MODEL WAS THEN REFINED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO AN ENHANCED RESOLUTION OF 1.90 ANGSTROM.
Resolution: 1.9→28.736 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.428 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 45-46 ARE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAPS. THEY WERE NOT MODELED. 5. TWO GLYCEROLS, ONE ACETATE, ONE CL ION FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 6. A ZN ATOM OF THE SUBUNIT IN THE ASYMMETRIC UNIT IS COORDINATED TO THE SIDE CHAINS OF HIS 116, GLU 139, CYS 142 AND CYS 150. X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT OF THE ZINC ION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.245
743
5 %
RANDOM
Rwork
0.189
-
-
-
all
0.192
-
-
-
obs
0.192
14719
99.35 %
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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: MASK
Displacement parameters
Biso mean: 24.066 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.27 Å2
0.63 Å2
0 Å2
2-
-
1.27 Å2
0 Å2
3-
-
-
-1.9 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→28.736 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1263
0
18
81
1362
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
1369
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
960
X-RAY DIFFRACTION
r_angle_refined_deg
1.615
2
1846
X-RAY DIFFRACTION
r_angle_other_deg
0.954
3
2373
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.228
5
168
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
42.677
26.316
57
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.509
15
263
X-RAY DIFFRACTION
r_chiral_restr
0.095
0.2
198
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1490
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
253
X-RAY DIFFRACTION
r_nbd_refined
0.207
0.2
281
X-RAY DIFFRACTION
r_nbd_other
0.169
0.2
919
X-RAY DIFFRACTION
r_nbtor_refined
0.185
0.2
649
X-RAY DIFFRACTION
r_nbtor_other
0.09
0.2
673
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.196
0.2
57
X-RAY DIFFRACTION
r_metal_ion_refined
0.097
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.226
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.154
0.2
58
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.177
0.2
14
X-RAY DIFFRACTION
r_mcbond_it
1.579
2
934
X-RAY DIFFRACTION
r_mcbond_other
0.342
2
327
X-RAY DIFFRACTION
r_mcangle_it
2.231
3
1350
X-RAY DIFFRACTION
r_scbond_it
1.579
2
602
X-RAY DIFFRACTION
r_scangle_it
2.251
3
496
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.307
57
-
Rwork
0.26
939
-
obs
-
996
93.52 %
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
1.1489
-0.8211
0.5308
2.4361
0.455
2.6683
-0.05
-0.0986
-0.0299
0.0008
0.046
-0.1223
0.0502
0.1773
0.004
-0.1101
0.0911
0.0322
-0.0121
-0.0017
-0.0537
17.0958
18.4295
0.0775
2
0.787
-0.3261
-0.1572
1.6731
0.0647
2.8665
-0.0402
-0.1329
0.0156
0.2617
0.0954
0.0346
-0.0922
0.012
-0.0552
-0.0831
0.1191
-0.0018
-0.0132
-0.0075
-0.0611
8.6948
24.2862
17.4951
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
0 - 44
1 - 45
2
2
47 - 158
48 - 159
+
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