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- PDB-5k7o: MicroED structure of lysozyme at 1.8 A resolution -

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Entry
Database: PDB / ID: 5k7o
TitleMicroED structure of lysozyme at 1.8 A resolution
DescriptorLysozyme C (E.C.3.2.1.17)
KeywordsHYDROLASE / Hydrolase
Specimen sourceGallus gallus / bird / Chicken / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
MethodElectron crystallography (1.8 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 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

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: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4254
Polyers14,3311
Non-polymers943
Water1,56787
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)360
ΔGint (kcal/M)-29
Surface area (Å2)6350
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)76.232, 76.232, 37.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2

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Components

#1: Polypeptide(L)Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1
Source: (natural) Gallus gallus / bird / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
References: UniProt: P00698, EC: 3.2.1.17

Cellular component

Molecular function

Biological process

#2: ChemicalChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Formula: Cl
#3: ChemicalChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na
#4: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: Lysozyme / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.014386 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Gallus gallus
Buffer solutionpH: 4.7
Buffer component
IDConc.UnitsNameFormulaBuffer ID
11.7Msodium chlorideNaCl1
250mMsodium acetateNaC2H3O21
SpecimenConc.: 25 mg/ml / Embedding 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: 1058 / Number of grids imaged: 2 / Number of real images: 1058
Image scansSampling size: 0.0311999992 microns / Dimension width: 2048 / Dimension height: 2048
EM diffractionCamera length: 1500 mm
EM diffraction shellFourier space coverage: 91.8 / High resolution: 1.8 Å / Low resolution: 2.06 Å / Multiplicity: 1.8 / Number of structure factors: 3170 / Phase residual: 46.4 deg.
EM diffraction statsFourier space coverage: 82.5 / High resolution: 1.5 Å / Number of intensities measured: 100693 / Number of structure factors: 14955 / Overall phase error: 29.91 deg. / Overall phase residual: 47.6 deg. / Phase error rejection criteria: 0 / R merge: 0.618 / R sym: 0.618
ReflectionD resolution high: 1.5 Å / D resolution low: 30.58 Å / Number all: 100693 / Number obs: 14955 / Rmerge I obs: 0.618 / Rpim I all: 0.26 / NetI over sigmaI: 2.7 / Redundancy: 6.7 / Percent possible obs: 82.5
Reflection shell
Rmerge I obsHighest resolutionLowest resolutionNumber unique allNumber unique obsRpim I allNetI over sigmaI obsRedundancyPercent possible all
3.0431.501.532822072.8740.31.424.2
0.1778.2130.5810491440.0628.57.397.1

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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
7MOLREP11.4.05OTHERphasing
8phenix.refine1.10_2155MODEL REFINEMENT1
9MOLREP11.4.05MOLECULAR REPLACEMENT1
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: 76.1 Å / Length b: 76.1 Å / Length c: 36.8 Å / Space group name: P 43 21 2 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 1.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 3J6K
Pdb chain ID: A / Pdb chain residue range: 1-129
RefineOverall SU ML: 0.27 / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 29.91
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.2842 / R factor R work: 0.2395 / R factor obs: 0.2416 / Highest resolution: 1.8 Å / Lowest resolution: 30.584 Å / Number reflection R free: 468 / Number reflection obs: 10275 / Percent reflection R free: 4.55 / Percent reflection obs: 96.83
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0041025
ELECTRON CRYSTALLOGRAPHYf_angle_d0.6091389
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d10.817611
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.041144
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.003181
Refine LS shell

Refine ID: ELECTRON CRYSTALLOGRAPHY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.80010.37940.32332.0605148302292.00
2.06050.32180.26862.59581563309100.00
2.59580.22880.192030.5884164347699.00

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