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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 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
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 (A2)360
ΔGint (kcal/M)-29
Surface area (A2)6350
MethodPISA
Unit cell
gamma
alpha
beta
Length a, b, c (A): 76.232, 76.232, 37.141 / Angle α, β, γ (deg.): 90.00, 90.00, 90.00

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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
#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 experimentReconstruction method: CRYSTALLOGRAPHY

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Sample preparation

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

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Data collection

MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
EM image scansSampling size: 0.0311999992 microns
ReflectionD resolution high: 1.5 A / D resolution low: 30.58 A / 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
ComputingStructure refinement: PHENIX (1.10_2155: ???)
3D reconstructionResolution: 1.8 A / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 3J6K
Pdb chain id: A
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 A / Solvent vdw probe radii: 1.11 A
Least-squares processR factor R free: 0.2842 / R factor R work: 0.2395 / R factor obs: 0.2416 / Highest resolution: 1.8 A / Lowest resolution: 30.584 A / 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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