Mass: 22022.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The 3 first amino acids are left over from TEV cleavage scar Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria) Strain: K96243 / Gene: dsbA, BPSL0381 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q63Y08
Resolution: 1.84→46.61 Å / SU ML: 0.2374 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0311 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Cycle of automated refinement with Phenix refine, using geometry and ADP weight optimisation. TLS (3 groups: residues 7-70, 71-137 and 138-197). Occupancy of the ligand was set to 0.5 and ...Details: Cycle of automated refinement with Phenix refine, using geometry and ADP weight optimisation. TLS (3 groups: residues 7-70, 71-137 and 138-197). Occupancy of the ligand was set to 0.5 and then refined using occupancy refinement. Manual refinement using coot V 0.9.5
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.194
1992
8.62 %
Random
Rwork
0.165
21119
-
-
obs
0.1701
23063
98.71 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 37.15 Å2
Refinement step
Cycle: LAST / Resolution: 1.84→46.61 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1494
0
13
206
1713
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
1587
X-RAY DIFFRACTION
f_angle_d
0.8374
2165
X-RAY DIFFRACTION
f_chiral_restr
0.0531
235
X-RAY DIFFRACTION
f_plane_restr
0.0072
284
X-RAY DIFFRACTION
f_dihedral_angle_d
15.6181
584
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.84-1.88
0.3959
116
0.3689
1379
X-RAY DIFFRACTION
90.72
1.88-1.93
0.301
137
0.2805
1475
X-RAY DIFFRACTION
98.59
1.93-1.99
0.275
147
0.2281
1489
X-RAY DIFFRACTION
98.85
1.99-2.05
0.2255
138
0.1956
1493
X-RAY DIFFRACTION
98.91
2.05-2.13
0.2265
141
0.1759
1497
X-RAY DIFFRACTION
99.15
2.13-2.21
0.2214
152
0.1768
1471
X-RAY DIFFRACTION
99.33
2.21-2.31
0.2045
136
0.173
1507
X-RAY DIFFRACTION
99.52
2.31-2.43
0.209
139
0.1735
1503
X-RAY DIFFRACTION
99.45
2.43-2.59
0.2267
147
0.1675
1521
X-RAY DIFFRACTION
99.52
2.59-2.79
0.2168
142
0.1636
1527
X-RAY DIFFRACTION
99.7
2.79-3.07
0.2203
143
0.1854
1519
X-RAY DIFFRACTION
99.76
3.07-3.51
0.1825
152
0.158
1552
X-RAY DIFFRACTION
99.82
3.51-4.42
0.1495
146
0.1355
1548
X-RAY DIFFRACTION
99.53
4.42-46.61
0.172
156
0.1537
1638
X-RAY DIFFRACTION
99.06
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
2.72784402708
0.154152243429
-0.0343096716141
4.51975191105
0.841581156973
2.29444583893
0.0292452018423
0.16398618451
-0.336327631379
0.142644910808
0.0497592410651
-0.0822834285348
0.233149921504
-0.00453667546246
-0.0762381034819
0.204112124533
-0.00168211012615
-0.0300910395732
0.258337197568
-0.0472703041368
0.206869867245
3.65725777819
-24.3385411747
-4.96911904385
2
6.41801351279
-0.619965706995
0.197233047235
3.688020207
1.27315194506
4.45314999141
-0.0435102016111
-0.244024691319
0.703016659571
0.00564139564641
0.0161496618692
0.0318955674196
-0.338294763125
-0.182292945298
0.0258275598091
0.233899260922
0.0485235508814
-0.00230796341569
0.219499154097
-0.0263662763149
0.27419406997
3.92690114276
-3.03251853423
0.778351847274
3
4.19369208379
2.82518864613
0.598940630439
5.14644599855
1.67435444388
1.15333404765
-0.0350381126959
0.379138923817
-0.372164542929
-0.0207474388024
0.0686515938999
-0.357348321687
0.0628519793031
0.00455981422427
-0.0102018404909
0.233233599846
0.0307568617573
-0.00547915783367
0.305877717584
-0.0400128670976
0.23055586474
7.53326676803
-23.7227951756
-8.35425920152
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
ID
Refine TLS-ID
Selection details
Auth seq-ID
Label seq-ID
1
1
chainAand (resid7:70)
7 - 70
1 - 64
2
2
chainAand (resid71:137)
71 - 137
65 - 131
3
3
chainAand (resid138:197)
138 - 197
132 - 191
+
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