Num. of mol.: 1 / Source method: obtained synthetically
Sequence details
RESIDUES A161-A167 THAT ARE PRESENT IN COORDINATES ARE LIKELY PART OF ENTITY 1. THEY WERE MODELED ...RESIDUES A161-A167 THAT ARE PRESENT IN COORDINATES ARE LIKELY PART OF ENTITY 1. THEY WERE MODELED AS POLY-ALA. THEIR ASSIGNMENT TO THE AMINO ACID SEQUENCE OF THE PROTEIN IS UNKNOWN DUE TO LACK OF CONTINUOUS ELECTRON DENSITY.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 4.32 Å3/Da / Density % sol: 71.53 %
Resolution: 2.6→28.513 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.863 / WRfactor Rfree: 0.298 / WRfactor Rwork: 0.263 / SU B: 25.513 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Atomic B-factors are residuals from TLS refinement. 3. Programs coot, molprobity, ffas03, SCWRL have also been used in refinement. 4. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Atomic B-factors are residuals from TLS refinement. 3. Programs coot, molprobity, ffas03, SCWRL have also been used in refinement. 4. Residues A 161 through A 167 are likely part of entity 1. They were modeled as poly-Ala due to insufficient electron density. Their assignment to the amino acid sequence is unknown due to lack of continuous electron density.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3
1433
5.062 %
RANDOM
Rwork
0.266
-
-
-
obs
0.267
28308
99.546 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 48.663 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.044 Å2
0.022 Å2
0 Å2
2-
-
0.044 Å2
0 Å2
3-
-
-
-0.067 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→28.513 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3167
0
3
0
3170
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
3245
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
2184
X-RAY DIFFRACTION
r_angle_refined_deg
1.053
1.963
4392
X-RAY DIFFRACTION
r_angle_other_deg
0.815
3.002
5306
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.211
5
399
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.79
23.537
147
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.03
15
547
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.059
15
21
X-RAY DIFFRACTION
r_chiral_restr
0.057
0.2
488
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
3597
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
667
X-RAY DIFFRACTION
r_nbd_refined
0.218
0.2
709
X-RAY DIFFRACTION
r_nbd_other
0.173
0.2
2152
X-RAY DIFFRACTION
r_nbtor_refined
0.179
0.2
1577
X-RAY DIFFRACTION
r_nbtor_other
0.082
0.2
1579
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.133
0.2
57
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.001
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.197
0.2
11
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.227
0.2
18
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.063
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
0.342
1.5
2066
X-RAY DIFFRACTION
r_mcbond_other
0.052
1.5
806
X-RAY DIFFRACTION
r_mcangle_it
0.576
2
3215
X-RAY DIFFRACTION
r_scbond_it
0.792
3
1346
X-RAY DIFFRACTION
r_scangle_it
1.241
4.5
1177
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection all
% reflection obs (%)
2.6-2.667
0.444
99
0.421
1968
2095
98.663
2.667-2.74
0.443
102
0.366
1863
1984
99.042
2.74-2.819
0.363
96
0.331
1868
1978
99.292
2.819-2.904
0.336
86
0.3
1823
1918
99.531
2.904-2.999
0.316
91
0.286
1758
1853
99.784
2.999-3.103
0.291
89
0.261
1693
1789
99.609
3.103-3.218
0.321
87
0.276
1645
1737
99.712
3.218-3.348
0.285
89
0.266
1572
1663
99.88
3.348-3.495
0.29
71
0.253
1552
1623
100
3.495-3.662
0.282
82
0.251
1432
1515
99.934
3.662-3.857
0.307
75
0.266
1389
1464
100
3.857-4.086
0.319
71
0.263
1328
1401
99.857
4.086-4.362
0.326
63
0.246
1241
1305
99.923
4.362-4.702
0.269
65
0.238
1150
1218
99.754
4.702-5.137
0.212
59
0.235
1063
1122
100
5.137-5.72
0.272
60
0.251
975
1035
100
5.72-6.562
0.369
55
0.295
849
904
100
6.562-7.932
0.295
43
0.27
762
805
100
7.932-10.807
0.266
31
0.234
584
620
99.194
10.807-28.513
0.277
19
0.288
360
408
92.892
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
5.1053
1.0507
-1.9672
1.0828
-0.6816
1.6257
-0.0362
-0.2221
-0.167
0.1175
-0.1364
-0.1185
0.0647
0.206
0.1726
-0.0572
0.0151
0.036
-0.098
-0.0171
-0.1771
-2.3132
67.0689
-0.0287
2
4.3119
0.9578
-0.0027
3.0188
-1.079
3.515
-0.1684
0.4739
-0.5878
-0.4859
0.0966
-0.0727
0.3836
-0.066
0.0718
0.0295
-0.049
0.1072
-0.0767
-0.1838
0.0276
-30.1975
48.8915
-8.4562
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
14 - 262
18 - 266
2
X-RAY DIFFRACTION
2
A
A
263 - 455
267 - 459
+
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