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- PDB-8t86: Racemic mixture of amylin segment 25-AILSS-29 forms heterochiral ... -

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Basic information

Entry
Database: PDB / ID: 8t86
TitleRacemic mixture of amylin segment 25-AILSS-29 forms heterochiral rippled beta-sheet
ComponentsRacemic mixture of amylin segment 25-AILSS-29
KeywordsPROTEIN FIBRIL / Rippled beta sheet / amyloid fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.102 Å
AuthorsSawaya, M.R. / Raskatov, J.A. / Hazari, A. / Sajimon, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG074954 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Racemic Peptides from Amyloid beta and Amylin Form Rippled beta-Sheets Rather Than Pleated beta-Sheets.
Authors: Hazari, A. / Sawaya, M.R. / Sajimon, M. / Vlahakis, N. / Rodriguez, J. / Eisenberg, D. / Raskatov, J.A.
History
DepositionJun 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Racemic mixture of amylin segment 25-AILSS-29


Theoretical massNumber of molelcules
Total (without water)4901
Polymers4901
Non-polymers00
Water905
1
A: Racemic mixture of amylin segment 25-AILSS-29

A: Racemic mixture of amylin segment 25-AILSS-29

A: Racemic mixture of amylin segment 25-AILSS-29

A: Racemic mixture of amylin segment 25-AILSS-29

A: Racemic mixture of amylin segment 25-AILSS-29

A: Racemic mixture of amylin segment 25-AILSS-29


Theoretical massNumber of molelcules
Total (without water)2,9376
Polymers2,9376
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_566-x,-y+1,-z+11
crystal symmetry operation2_466-x-1,-y+1,-z+11
crystal symmetry operation2_666-x+1,-y+1,-z+11
Unit cell
Length a, b, c (Å)9.500, 9.880, 16.290
Angle α, β, γ (deg.)90.452, 98.132, 94.376
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide Racemic mixture of amylin segment 25-AILSS-29


Mass: 489.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.54 Å3/Da / Density % sol: 20.19 %
Crystal growTemperature: 298 K / Method: batch mode / Details: hexafluoroisopropanol, water

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→16.123 Å / Num. obs: 1898 / % possible obs: 80.3 % / Redundancy: 5.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.159 / Net I/σ(I): 4.86
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.1-1.160.9551010.6511.0671
1.16-1.230.8662020.7830.9691
1.23-1.310.5332570.9360.5931
1.31-1.420.4892890.9270.5441
1.42-1.560.3232380.9750.3591
1.56-1.740.2762290.9690.3081
1.74-2.010.1661990.9850.1861
2.01-2.460.1351780.980.1531
2.46-3.480.1141310.9890.1271
3.48-16.1230.112740.9920.1241

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.102→16.123 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.826 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.033
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1793 190 10.016 %
Rwork0.1517 1707 -
all0.154 --
obs-1897 80.723 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.265 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.123 Å2-1.105 Å2
2--0.488 Å2-0.219 Å2
3---0.305 Å2
Refinement stepCycle: LAST / Resolution: 1.102→16.123 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms34 0 0 5 39
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01333
X-RAY DIFFRACTIONr_bond_other_d0.0010.01737
X-RAY DIFFRACTIONr_angle_refined_deg0.7541.62644
X-RAY DIFFRACTIONr_angle_other_deg0.2871.62185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.79554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.424156
X-RAY DIFFRACTIONr_chiral_restr0.0330.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0236
X-RAY DIFFRACTIONr_gen_planes_other00.024
X-RAY DIFFRACTIONr_nbd_refined0.1040.23
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1520.223
X-RAY DIFFRACTIONr_nbtor_refined0.1230.216
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0570.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0180.21
X-RAY DIFFRACTIONr_nbd_other0.160.28
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0940.24
X-RAY DIFFRACTIONr_mcbond_it0.8381.12519
X-RAY DIFFRACTIONr_mcbond_other0.8291.10518
X-RAY DIFFRACTIONr_mcangle_it1.0131.67322
X-RAY DIFFRACTIONr_mcangle_other0.9961.68823
X-RAY DIFFRACTIONr_scbond_it0.8341.20114
X-RAY DIFFRACTIONr_scbond_other0.6981.17413
X-RAY DIFFRACTIONr_scangle_it1.1341.77522
X-RAY DIFFRACTIONr_scangle_other1.1521.78122
X-RAY DIFFRACTIONr_lrange_it4.716.16932
X-RAY DIFFRACTIONr_lrange_other4.94515.20827
X-RAY DIFFRACTIONr_rigid_bond_restr0.386369
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.102-1.2310.359310.3242770.3286570.9180.91346.87980.294
1.231-1.420.288540.2294860.2345950.940.96890.75630.214
1.42-1.7360.188460.1844200.1844940.9810.97894.3320.17
1.736-2.4410.151380.1293380.1313940.9890.9995.43150.142
2.441-16.1230.134210.1161860.1172100.9890.98598.57140.146

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