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- PDB-5k7p: MicroED structure of xylanase at 2.3 A resolution -

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Basic information

Entry
Database: PDB / ID: 5k7p
TitleMicroED structure of xylanase at 2.3 A resolution
DescriptorEndo-1,4-beta-xylanase 2 (E.C.3.2.1.8)
KeywordsHYDROLASE / Hydrolase
Specimen sourceHypocrea jecorina / fungus / Trichoderma reesei
MethodElectron crystallography (2.3 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: Endo-1,4-beta-xylanase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1093
Polyers20,8551
Non-polymers2542
Water41423
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (A2)240
ΔGint (kcal/M)0
Surface area (A2)8010
MethodPISA
Unit cell
gamma
alpha
beta
Length a, b, c (A): 48.161, 59.752, 69.812 / Angle α, β, γ (deg.): 90.00, 90.00, 90.00

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Components

#1: Polypeptide(L)Endo-1,4-beta-xylanase 2 / Xylanase 2 / 1 / 4-beta-D-xylan xylanohydrolase 2


Mass: 20855.467 Da / Num. of mol.: 1 / Source: (natural) Hypocrea jecorina / fungus / References: UniProt: P36217, EC: 3.2.1.8
#2: ChemicalChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Formula: I
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: Xylanase / 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: 1.9 A / D resolution low: 25.55 A / Number all: 38699 / Number obs: 10664 / Rmerge I obs: 0.428 / Rpim I all: 0.245 / NetI over sigmaI: 2.7 / Redundancy: 3.6 / Percent possible obs: 66.6
Reflection shell
Rmerge I obsHighest resolutionLowest resolutionNumber unique allNumber unique obsRpim I allNetI over sigmaI obsRedundancyPercent possible all
2.4771.901.943482142.2140.41.620.4
0.1228.9125.555841510.0647.13.984.6

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Processing

SoftwareName: PHENIX / Version: (1.10_2155: ???) / Classification: refinement
ComputingStructure refinement: PHENIX (1.10_2155: ???)
3D reconstructionResolution: 2.3 A / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 2DFB
Pdb chain id: A
RefineOverall SU ML: 0.42 / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 29.95 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 A / Solvent vdw probe radii: 1.11 A / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.267 / R factor R work: 0.2295 / R factor obs: 0.2313 / Highest resolution: 2.3 A / Lowest resolution: 25.549 A / Number reflection R free: 369 / Number reflection obs: 7734 / Percent reflection R free: 4.77 / Percent reflection obs: 82.44
Refine LS restraints
Refine idTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0021527
ELECTRON CRYSTALLOGRAPHYf_angle_d0.4962084
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d10.687841
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.043207
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.003275
Refine LS shell

Refine id: ELECTRON CRYSTALLOGRAPHY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.30000.38950.35402.632688219775.00
2.63260.32360.27313.3156146254687.00
3.31560.20140.167525.5508135262285.00

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