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- PDB-5vos: VGSNKGAIIGL from Amyloid Beta determined by MicroED -

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Entry
Database: PDB / ID: 5vos
TitleVGSNKGAIIGL from Amyloid Beta determined by MicroED
DescriptorAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / Amyloid / steric zipper
Specimen sourceHomo sapiens / human
MethodElectron crystallography (1.42 Å resolution / 3d array / Crystallography / Molecular replacement)
AuthorsRodriguez, J.A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.S. / Griner, S.L. / Gonen, T.
CitationJ. Biol. Chem., 2017

J. Biol. Chem., 2017 Yorodumi Papers
Common fibrillar spines of amyloid-β and human Islet Amyloid Polypeptide revealed by Micro Electron Diffraction and inhibitors developed using structure-based design.
Pascal Krotee / Sarah L Griner / Michael R Sawaya / Duilio Cascio / Jose A Rodriguez / Dan Shi / Stephan Philipp / Kevin Murray / Lorena Saelices / Ji Lee / Paul Seidler / Charles G Glabe / Lin Jiang / Tamir Gonen / David S Eisenberg

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 3, 2017 / Release: Jan 3, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 3, 2018Structure modelrepositoryInitial release
1.1Jan 10, 2018Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

Deposited unit
A: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)1,0291
Polyers1,0291
Non-polymers00
Water181
#1
A: Amyloid beta A4 protein

A: Amyloid beta A4 protein

A: Amyloid beta A4 protein

A: Amyloid beta A4 protein

A: Amyloid beta A4 protein

A: Amyloid beta A4 protein

A: Amyloid beta A4 protein

A: Amyloid beta A4 protein

A: Amyloid beta A4 protein

A: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)10,29210
Polyers10,29210
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation2_658-x+1,y+1/2,-z+31
crystal symmetry operation2_668-x+1,y+3/2,-z+31
crystal symmetry operation2_678-x+1,y+5/2,-z+31
crystal symmetry operation2_648-x+1,y-1/2,-z+31
crystal symmetry operation2_638-x+1,y-3/2,-z+31
Unit cell
γ
α
β
Length a, b, c (Å)18.780, 4.730, 33.470
Angle α, β, γ (deg.)90.000, 100.020, 90.000
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Polypeptide(L)Amyloid beta A4 protein


Mass: 1029.213 Da / Num. of mol.: 1
Fragment: VGSNKGAIIGL peptide (residues 24-34, UNP residues 7-17)
Source: (synth.) Homo sapiens / human / References: UniProt: L7XCZ9
#2: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / Reconstruction method: CRYSTALLOGRAPHY

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Sample preparation

ComponentName: Fibrils of Amyloid Beta segment 24-34 / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
EM crystal formationInstrument: microcentrifuge tube / Atmosphere: air / Details: shaking / Temperature: 310 kelvins / Time: 2 sec. / Time unit: DAY
Buffer solutionpH: 4
Buffer component
IDConc.UnitsNameBuffer ID
125mMcitric acid1
25%DMSO1
SpecimenConc.: 7.5 mg/ml / Details: nanocrystals / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
CrystalDensity Matthews: 1.42
Crystal growTemp: 310 K / Method: Batch / pH: 4 / Details: 50 mM sodium citrate, pH 4.0, 10% v/v DMSO

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 0.03 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number of diffraction images: 471
Image scansDimension width: 2048 / Dimension height: 2048
EM diffractionCamera length: 1840 mm
EM diffraction shellFourier space coverage: 47.5 / High resolution: 1.42 Å / Low resolution: 1.49 Å / Multiplicity: 2.6 / Number of structure factors: 84 / Phase residual: 0.01 deg.
EM diffraction statsFourier space coverage: 85.5 / High resolution: 1.42 Å / Number of intensities measured: 5843 / Number of structure factors: 1129 / Overall phase error: 0 deg. / Overall phase residual: 0.01 deg. / Phase error rejection criteria: 0 / R merge: 0.222 / R sym: 0.222
DiffractionMean temperature: 100 kelvins
SourceSource: TRANSMISSION ELECTRON MICROSCOPE / Type: TECNAI F20 TEM / Wavelength: 0.0251
DetectorType: TVIPS F416 CMOS CAMERA / Detector: CMOS DETECTOR / Collection date: Apr 17, 2015
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 14.635 Å2 / D resolution high: 1.42 Å / D resolution low: 32.96 Å / Number obs: 1129 / Observed criterion sigma I: -3 / CC half: 0.98 / Rmerge I obs: 0.222 / Rrim I all: 0.244 / Chi squared: 0.926 / NetI over sigmaI: 4.88 / Number measured all: 5843 / Redundancy: 5.175 / Scaling rejects: 33 / Percent possible obs: 85.5
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured obsNumber possibleNumber unique obsCC halfRrim I allRedundancyPercent possible all
0.4961.4201.4901.090216177840.4520.6112.57147.500
0.3151.4901.5703.1005621811360.8990.3544.13275.100
0.3881.5701.6702.2403801301060.8550.4433.58581.500
0.4211.6701.7802.6605071331150.6540.4794.40986.500
0.3431.7801.9203.7406981311270.9770.3765.49696.900
0.2641.9202.1105.8308991341330.9770.2856.75999.300
0.2732.1102.3606.6409491311290.9420.2967.35798.500
0.2092.3602.7206.20047486860.9900.2315.512100.000
0.2142.7203.3307.02046986860.9220.2385.453100.000
0.1713.3304.72010.09054489880.9760.1846.18298.900
0.1384.72032.9608.34014542390.9890.1613.71892.900

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Phasing

PhasingMethod: MR

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Processing

Software
NameVersionClassificationContact authorLocationTypeContact author emailLanguageDate
XSCALEdata scalingWolfgang Kabschhttp://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.htmlpackage
PHASERmolecular replacementRandy J. Readhttp://www-structmed.cimr.cam.ac.uk/phaser/programcimr-phaser@lists.cam.ac.uk
REFMACrefinementGarib N. Murshudovhttp://www.ccp4.ac.uk/dist/html/refmac5.htmlprogramgarib@ysbl.york.ac.ukFortran_77
PDB_EXTRACT3.22data extractionPDBhttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packagedeposit@deposit.rcsb.orgC++July. 13, 2016
XDSdata reduction
PHASERphasing
EM software
IDNameVersionCategoryImaging IDFitting IDImage processing ID
1TVIPS TemCam-F416IMAGE ACQUISITION1
6CootMODEL FITTING1
8phaserMOLECULAR REPLACEMENT1
11XSCALEJun 17, 2015CRYSTALLOGRAPHY MERGING1
13Refmac5MODEL REFINEMENT1
EM 3D crystal entityAngle alpha: 90 deg. / Angle beta: 100.017 deg. / Angle gamma: 90 deg. / Length a: 18.78 Å / Length b: 4.73 Å / Length c: 33.47 Å / Space group name: P 21 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL / Target criteria: Maximum likelihood
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Correlation coeff Fo to Fc: 0.933 / Correlation coeff Fo to Fc free: 0.881
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Overall SU B: 2.871 / Overall SU ML: 0.1 / Overall SU R Cruickshank DPI: 0.1152 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.115 / Overall ESU R Free: 0.122
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso max: 42.18 Å2 / B iso mean: 13.166 Å2 / B iso min: 4.42 Å2 / Aniso B11: 1.04 Å2 / Aniso B12: - Å2 / Aniso B13: 0.83 Å2 / Aniso B22: -1.3 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.04 Å2
Least-squares processR factor R free: 0.2924 / R factor R work: 0.2335 / R factor obs: 0.2389 / Highest resolution: 1.42 Å / Lowest resolution: 32.96 Å / Number reflection R free: 113 / Number reflection obs: 1014 / Percent reflection R free: 1 / Percent reflection obs: 85.51
Refine hist #finalHighest resolution: 1.42 Å / Lowest resolution: 32.96 Å / B iso mean solvent: 15.91 / Number residues total: 11
Number of atoms included #finalProtein: 72 / Nucleic acid: 0 / Ligand: 0 / Solvent: 1 / Total: 73
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0160.01971
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0030.02081
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.8382.04094
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.6593.000185
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg8.7145.00010
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg52.25630.0001
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg15.73415.00013
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0760.20012
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0050.02080
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0000.02012
Refine LS shellHighest resolution: 1.422 Å / R factor R free: 0.434 / R factor R free error: 0 / R factor R work: 0.367 / Lowest resolution: 1.459 Å / Number reflection R free: 4 / Number reflection R work: 38 / Number reflection all: 42 / Total number of bins used: 20 / Percent reflection obs: 42

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