BaculoviralIAPrepeat-containingprotein7, BaculoviralIAPrepeat-containingprotein4 / Kidney inhibitor of apoptosis protein / KIAP / Livin / Melanoma inhibitor of apoptosis protein / ML- ...Kidney inhibitor of apoptosis protein / KIAP / Livin / Melanoma inhibitor of apoptosis protein / ML-IAP / RING finger protein 50 / E3 ubiquitin-protein ligase XIAP / IAP-like protein / ILP / hILP / Inhibitor of apoptosis protein 3 / IAP-3 / hIAP-3 / hIAP3 / X-linked inhibitor of apoptosis protein / X-linked IAP
Mass: 13072.521 Da / Num. of mol.: 2 / Fragment: BIR domain 63-179 / Mutation: S150G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344, API3, BIRC4, IAP3, XIAP Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96CA5, UniProt: P98170
Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
-
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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion / pH: 6 Details: Protein at 25 mg/mL in 10 mM MES was mixed with peptide (AVPW)n a 1:2 protein/peptide ratio. The MLIAP peptide complex was mixed with crystallization well solution (100 mM Bis ...Details: Protein at 25 mg/mL in 10 mM MES was mixed with peptide (AVPW)n a 1:2 protein/peptide ratio. The MLIAP peptide complex was mixed with crystallization well solution (100 mM Bis tris(hydroxymethyl)aminomethane (tris), pH 6; 200 mM lithium sulfate; 20 25% (w/v) poly(ethylene glycol) 3350) in a ratio of 1 uL of protein complex to 1 uL of well solution, VAPOR DIFFUSION, temperature 292K
Resolution: 1.71→1.77 Å / Redundancy: 8 % / Mean I/σ(I) obs: 4 / Num. unique all: 3045 / Rsym value: 0.346 / % possible all: 100
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Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
PHASER
phasing
REFMAC
5.6.0117
refinement
DENZO
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.274 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1658
1557
5 %
RANDOM
Rwork
0.15609
-
-
-
all
0.15656
31343
-
-
obs
0.15656
31303
99.8 %
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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: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 22.935 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.74 Å2
0 Å2
0 Å2
2-
-
-0.74 Å2
-0 Å2
3-
-
-
1.48 Å2
Refinement step
Cycle: LAST / Resolution: 1.71→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1539
0
12
189
1740
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.02
1628
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1088
X-RAY DIFFRACTION
r_angle_refined_deg
1.138
1.98
2208
X-RAY DIFFRACTION
r_angle_other_deg
0.802
3.005
2604
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.736
5
182
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.245
22.911
79
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.182
15
222
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.233
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
205
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
1802
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
373
LS refinement shell
Resolution: 1.71→1.754 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.217
104
-
Rwork
0.188
1955
-
obs
-
-
99.42 %
Refinement TLS params.
Method: refined / Origin x: 81.3186 Å / Origin y: 63.9912 Å / Origin z: 36.1251 Å
11
12
13
21
22
23
31
32
33
T
0.0036 Å2
0.0021 Å2
0.0095 Å2
-
0.0145 Å2
-0.0036 Å2
-
-
0.0427 Å2
L
0.5455 °2
0.1116 °2
-0.3496 °2
-
1.3694 °2
-1.0159 °2
-
-
2.1807 °2
S
0.0163 Å °
0.0517 Å °
-0.0181 Å °
-0.0214 Å °
-0.0142 Å °
0.0057 Å °
-0.0093 Å °
-0.0236 Å °
-0.0021 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
78 - 167
2
X-RAY DIFFRACTION
1
B
78 - 169
+
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