SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: 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.
Resolution: 2.01→29.5 Å / Num. obs: 22815 / % possible obs: 85.9 % / Redundancy: 3.49 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.06
Reflection shell
Resolution (Å)
% possible obs (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
2.01-2.08
46.8
0.398
1.97
2809
2077
1,2
2.08-2.17
57.7
0.37
2.47
5380
2852
1,2
2.17-2.26
83.8
0.307
3.2
7889
3527
1,2
2.26-2.38
88.4
0.344
3.96
11139
4049
1,2
2.38-2.53
92.5
0.339
5.06
14966
4299
1,2
2.53-2.73
95
0.273
6.77
18378
4408
1,2
2.73-3
97.7
0.212
9.73
24691
4409
1,2
3-3.43
98.6
0.119
15.98
31005
4504
1,2
3.43-4.32
99.8
0.08
21.69
31522
4583
1,2
4.32-29.5
99.4
0.057
28.35
31169
4610
1,2
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
XSCALE
datascaling
PDB_EXTRACT
1.601
dataextraction
XDS
datareduction
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.01→29.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.396 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.173 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE PEPTIDE BOND BETWEEN ASP 166 AND ASP 167 NEAR THE PUTATIV ACTIVE SITE WAS MODELED IN THE CIS CONFORMATION 3.ELECTRON DENSITIES ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE PEPTIDE BOND BETWEEN ASP 166 AND ASP 167 NEAR THE PUTATIV ACTIVE SITE WAS MODELED IN THE CIS CONFORMATION 3.ELECTRON DENSITIES BETWEEN RESIDUE RANGES 109-119,198-202, AND 279-291 WERE DISORDERED; THEREFORE, THESE REGIONS WERE NOT MODELED. 4. THE ELECTRON DENSITY MAP SHOWS SUBSTANTIAL DIFFERENCE DENSITY THE VICINITY OF LYS 249.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24423
1177
5.2 %
RANDOM
Rwork
0.20277
-
-
-
all
0.205
-
-
-
obs
0.20478
21615
93.81 %
-
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: 35.477 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.36 Å2
0 Å2
0 Å2
2-
-
0.44 Å2
0 Å2
3-
-
-
-4.8 Å2
Refinement step
Cycle: LAST / Resolution: 2.01→29.5 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2351
0
12
113
2476
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
2402
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.539
1.976
3251
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.08
5
307
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.192
24.737
95
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.251
15
395
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.835
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.102
0.2
378
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1781
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.205
0.2
1012
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.312
0.2
1686
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.131
0.2
128
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.185
0.2
34
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.122
0.2
8
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.941
3
1579
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.978
5
2486
X-RAY DIFFRACTION
r_scbond_it
5.021
8
923
X-RAY DIFFRACTION
r_scangle_it
7.038
11
765
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.01→2.059 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.356
57
-
Rwork
0.296
1137
-
obs
-
-
68 %
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
4.1015
-1.3436
-2.7752
1.0008
1.1901
2.8879
-0.0618
0.2389
-0.2399
-0.0332
-0.2241
0.3004
-0.1018
-0.3074
0.2859
0.002
-0.0296
-0.0553
0.049
-0.0332
0.1579
-5.553
39.833
53.943
2
0.6902
0.0597
-1.4973
1.246
0.2259
3.3499
-0.046
0.1142
0.0095
-0.0463
-0.1054
0.0407
-0.0898
-0.0795
0.1514
-0.0407
-0.0807
-0.0495
0.1092
0.0125
0.1159
10.673
35.25
51.601
3
0.592
0.1659
-0.853
4.1176
-1.6858
6.5179
0.0347
-0.2213
-0.1394
-0.0108
-0.0151
0.2128
0.5345
-0.0603
-0.0195
-0.0352
-0.0544
-0.0312
0.1393
0.0158
0.154
15.279
22.907
61.57
4
2.2327
0.2224
-2.4527
1.2091
0.6536
6.4413
-0.0664
-0.0791
0.0985
0.0333
0.032
-0.0531
-0.0388
0.2665
0.0344
0.0648
-0.0236
-0.0504
0.1259
0.0259
0.1208
15.911
31.671
57.152
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
0 - 152
1 - 153
2
X-RAY DIFFRACTION
2
A
A
153 - 223
154 - 224
3
X-RAY DIFFRACTION
3
A
A
224 - 292
225 - 293
4
X-RAY DIFFRACTION
4
A
A
293 - 339
294 - 340
+
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