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- PDB-5k7n: MicroED structure of tau VQIVYK peptide at 1.1 A resolution -

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Basic information

Entry
Database: PDB / ID: 5k7n
TitleMicroED structure of tau VQIVYK peptide at 1.1 A resolution
DescriptorVQIVYK
KeywordsPROTEIN FIBRIL / Amyloid
Specimen sourceHomo sapiens / human
MethodElectron crystallography (1.1 A resolution / Crystallography)
Authorsde la Cruz, M.J. / Hattne, J. / Shi, D. / Seidler, P. / Rodriguez, J. / Reyes, F.E. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. / Gonen, T.
CitationNat. Methods, 2017, 14, 399-402

Nat. Methods, 2017, 14, 399-402 StrPapers
Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.
M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen

DateDeposition: May 26, 2016 / Release: Apr 5, 2017 / Last modification: Apr 12, 2017

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Assembly

Deposited unit
Z: VQIVYK


Theoretical massNumber of molelcules
Total (without water)7501
Polyers7501
Non-polymers00
Water362
#1
Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK

Z: VQIVYK


Theoretical massNumber of molelcules
Total (without water)6,7499
Polyers6,7499
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_515x,y-4,z1
crystal symmetry operation1_525x,y-3,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_595x,y+4,z1
Unit cell
gamma
alpha
beta
Length a, b, c (A): 29.420, 4.990, 37.170 / Angle α, β, γ (deg.): 90.00, 111.55, 90.00
DetailsThe biological unit is an extended pair of beta sheets comprising peptides at position X,Y,Z extended ad infinitum along the b crystal axis.

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Components

#1: Polypeptide(L)VQIVYK / tau peptide


Mass: 749.917 Da / Num. of mol.: 1 / Source: (synth.) Homo sapiens / human
#2: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentReconstruction method: CRYSTALLOGRAPHY

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Sample preparation

ComponentName: VQIVYK / Type: ORGANELLE OR CELLULAR COMPONENT
VitrificationCryogen name: ETHANE

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Data collection

MicroscopyMicroscope model: FEI TECNAI F20 / Date: Apr 26, 2016
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
EM image scansSampling size: 0.0311999992 microns
ReflectionB iso Wilson estimate: 8.35 A^2 / D resolution high: 1.1 A / D resolution low: 14.7 A / Number all: 6185 / Number obs: 3319 / Rmerge I obs: 0.126 / Rsym value: 0.126 / NetI over sigmaI: 2.4 / Redundancy: 1.9 / Percent possible obs: 83
Reflection shellRmerge I obs: 0.472 / Highest resolution: 1.1 A / Lowest resolution: 1.23 A / Number unique all: 463 / Number unique obs: 255 / Rsym value: 0.472 / NetI over sigmaI obs: 1.1 / Redundancy: 1.8 / Percent possible all: 79.4

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
ComputingStructure refinement: BUSTER 2.10.0
3D reconstructionResolution: 1.1 A / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: RECIPROCAL
RefineCorrelation coeff Fo to Fc: 0.9486 / Correlation coeff Fo to Fc free: 0.9516 / Overall SU R Cruickshank DPI: 0.048 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall SU R Blow DPI: 0.046 / Overall SU R free Blow DPI: 0.046 / Overall SU R free Cruickshank DPI: 0.045
Displacement parametersB iso mean: 13.51 A2 / Aniso B11: 1.6602 A2 / Aniso B12: 0 A2 / Aniso B13: 3.1898 A2 / Aniso B22: 0.0678 A2 / Aniso B23: 0 A2 / Aniso B33: -1.728 A2
Least-squares processR factor R free: 0.2228 / R factor R work: 0.2097 / R factor obs: 0.211 / Highest resolution: 1.1 A / Lowest resolution: 14.7 A / Number reflection R free: 190 / Number reflection obs: 1898 / Percent reflection R free: 10.01 / Percent reflection obs: 81.11
Refine analyzeLuzzati coordinate error obs: 0.203 A
Refine LS restraints

Refine id: ELECTRON CRYSTALLOGRAPHY

TypeDev idealNumberRestraint functionWeight
t_bond_d0.012111HARMONIC2.00
t_angle_deg0.77202HARMONIC2.00
t_dihedral_angle_d26SINUSOIDAL2.00
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes2HARMONIC2.00
t_gen_planes12HARMONIC5.00
t_it111HARMONIC20.00
t_nbd0SEMIHARMONIC5.00
t_omega_torsion1.62
t_other_torsion9.65
t_improper_torsion
t_chiral_improper_torsion7SEMIHARMONIC5.00
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact68SEMIHARMONIC4.00
Refine LS shellHighest resolution: 1.1 A / R factor R free: 0.2243 / R factor R work: 0.2104 / R factor all: 0.2117 / Lowest resolution: 1.23 A / Number reflection R free: 54 / Number reflection R work: 489 / Number reflection all: 543 / Total number of bins used: 5 / Percent reflection R free: 9.94 / Percent reflection obs: 81.11
Refine TLSMethod: refined / L11: 0.4341 / L12: 0.2835 / L13: 0.124 / L22: 0.6654 / L23: 0.2447 / L33: 0.0381 / S11: -0.0138 / S12: 0.0028 / S13: 0.002 / S21: -0.0426 / S22: 0.0046 / S23: 0.0052 / S31: 0.028 / S32: 0.0029 / S33: 0.0092 / T11: -0.0041 / T12: -0.0004 / T13: 0.0615 / T22: -0.0667 / T23: -0.0046 / T33: 0.0721 / Origin x: 10.8417 A / Origin y: 1.956 A / Origin z: 8.5763 A
Refine TLS groupSelection details: { Z|* }

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