survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization ...survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization / chromosome passenger complex / cysteine-type endopeptidase inhibitor activity / nuclear chromosome / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cobalt ion binding / cytoplasmic microtubule / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic cytokinesis / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / tubulin binding / positive regulation of mitotic cell cycle / RHO GTPases Activate Formins / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / spindle microtubule / kinetochore / small GTPase binding / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Neddylation / mitotic cell cycle / midbody / protein-folding chaperone binding / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Resolution: 2.18→2.22 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 2.3 / Num. unique all: 586 / % possible all: 100
-
Processing
Software
Name
Version
Classification
HKL-3000
datacollection
HKL-3000
phasing
MLPHARE
phasing
REFMAC
5.6.0117
refinement
Coot
modelbuilding
HKL-3000
datareduction
HKL-3000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.18→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.5 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.159 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21488
554
4.8 %
RANDOM
Rwork
0.19838
-
-
-
all
0.19919
11061
-
-
obs
0.19919
11061
99.66 %
-
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: 56.691 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.31 Å2
0 Å2
0 Å2
2-
-
0.06 Å2
0 Å2
3-
-
-
-0.37 Å2
Refinement step
Cycle: LAST / Resolution: 2.18→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1138
0
40
53
1231
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.022
1199
X-RAY DIFFRACTION
r_bond_other_d
0.01
0.02
878
X-RAY DIFFRACTION
r_angle_refined_deg
1.675
1.98
1600
X-RAY DIFFRACTION
r_angle_other_deg
1.998
3.002
2125
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.314
5
140
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.223
24.386
57
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.65
15
204
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.769
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.098
0.2
162
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
1295
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
237
LS refinement shell
Resolution: 2.18→2.237 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.3
37
-
Rwork
0.258
723
-
obs
-
-
97.06 %
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
7.697
0.7332
-1.0087
4.2059
0.4184
2.6869
-0.1271
0.167
-0.7506
0.0029
0.1662
-0.3741
0.1962
0.038
-0.039
0.1749
0.0222
0.0049
0.1188
-0.0876
0.1319
-17.797
-13.837
-15.042
2
0.0731
-0.6443
-0.9658
6.1093
9.579
15.4563
-0.0012
-0.0127
-0.0205
-0.0113
0.1032
0.0336
0.0683
0.1603
-0.102
0.2201
-0.0554
0.0242
0.2261
-0.0878
0.0958
-31.777
-17.962
-21.306
3
23.064
11.0393
10.6602
8.5981
-5.7436
46.6643
0.2005
0.0623
-0.0639
-0.7566
-0.0554
-0.1187
0.4985
0.9705
-0.1451
1.1696
-0.1698
0.1972
0.1501
-0.0128
0.0396
-29.8
-33.562
-55.362
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
5 - 90
2
X-RAY DIFFRACTION
2
A
91 - 133
3
X-RAY DIFFRACTION
3
A
134 - 142
+
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