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- PDB-5k7q: MicroED structure of thaumatin at 2.5 A resolution -

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Entry
Database: PDB / ID: 5k7q
TitleMicroED structure of thaumatin at 2.5 A resolution
DescriptorThaumatin-1
KeywordsPLANT PROTEIN / Sweet protein
Specimen sourceThaumatococcus daniellii / plant / Katemfe
MethodElectron crystallography (2.5 Å resolution / 3d array / 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 Yorodumi Papers
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 26, 2016 / Release: Apr 5, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 5, 2017Structure modelrepositoryInitial release
1.1Apr 12, 2017Structure modelDatabase references

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Assembly

Deposited unit
A: Thaumatin-1


Theoretical massNumber of molelcules
Total (without water)22,2271
Polyers22,2271
Non-polymers00
Water32418
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)9550
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)58.118, 58.118, 150.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP 41 21 2

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Components

#1: Polypeptide(L)Thaumatin-1 / Thaumatin I


Mass: 22227.059 Da / Num. of mol.: 1 / Source: (natural) Thaumatococcus daniellii / plant / References: UniProt: P02883
#2: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: Thaumatin / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.022166 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Thaumatococcus daniellii
Buffer solutionpH: 7
Buffer componentConc.: 1.1 mg/ml / Units: M / Name: ammonium tartate
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 0.004 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number of diffraction images: 471 / Number of grids imaged: 3 / Number of real images: 471
Image scansSampling size: 0.0311999992 microns / Dimension width: 2048 / Dimension height: 2048
EM diffractionCamera length: 2000 mm
EM diffraction shellFourier space coverage: 92.2 / High resolution: 2.5 Å / Low resolution: 2.86 Å / Multiplicity: 3.9 / Number of structure factors: 2825 / Phase residual: 52.4 deg.
EM diffraction statsFourier space coverage: 81.5 / High resolution: 2.11 Å / Number of intensities measured: 51116 / Number of structure factors: 12786 / Overall phase error: 28.74 deg. / Overall phase residual: 41.7 deg. / Phase error rejection criteria: 0 / R merge: 0.434 / R sym: 0.434
ReflectionD resolution high: 2.11 Å / D resolution low: 27.73 Å / Number all: 51116 / Number obs: 12786 / Rmerge I obs: 0.434 / Rpim I all: 0.235 / NetI over sigmaI: 2.8 / Redundancy: 4 / Percent possible obs: 81.5
Reflection shell
Rmerge I obsHighest resolutionLowest resolutionNumber unique allNumber unique obsRpim I allNetI over sigmaI obsRedundancyPercent possible all
0.8642.112.1715636140.6361.22.548.0
0.1838.9327.738792210.0945.64.085.4

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Processing

SoftwareName: PHENIX / Version: (1.10_2155: ???) / Classification: refinement
EM software
IDNameVersionCategoryImaging IDFitting IDDetailsImage processing ID
1EM-Menu4.0.9.75IMAGE ACQUISITION1
5iMosflm/MOSFLM7.2.1DIFFRACTION INDEXING
6MOLREP11.4.05MODEL FITTING1
8phenix.refine1.10_2155MODEL REFINEMENT1
9MOLREP11.4.05MOLECULAR REPLACEMENTStarting model PDB ID 4ek01
11POINTLESS1.10.21SYMMETRY DETERMINATION1
12AIMLESS0.5.25CRYSTALLOGRAPHY MERGING1
EM 3D crystal entityAngle alpha: 90 deg. / Angle beta: 90 deg. / Angle gamma: 90 deg. / Length a: 57.78 Å / Length b: 57.78 Å / Length c: 149.7 Å / Space group name: P 41 21 2 / Space group num: 92
CTF correctionType: NONE
3D reconstructionResolution: 2.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 4EK0
Pdb chain ID: A / Pdb chain residue range: 1-207
RefineOverall SU ML: 0.48 / Cross valid method: FREE R-VALUE / Sigma F: 1.37 / Overall phase error: 28.74 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2945 / R factor R work: 0.2513 / R factor obs: 0.2535 / Highest resolution: 2.5 Å / Lowest resolution: 27.732 Å / Number reflection R free: 453 / Number reflection obs: 8898 / Percent reflection R free: 5.09 / Percent reflection obs: 93.56
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0021595
ELECTRON CRYSTALLOGRAPHYf_angle_d0.4622168
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d12.505960
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.039230
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.004285
Refine LS shell

Refine ID: ELECTRON CRYSTALLOGRAPHY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.50010.38980.34082.8615135269092.00
2.86150.31270.26363.6040148284596.00
3.60400.23840.195927.7333170291093.00

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