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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 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: 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 (Å2)240
ΔGint (kcal/M)0
Surface area (Å2)8010
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)48.161, 59.752, 69.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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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

Cellular component

Molecular function

Biological process

#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 experimentAggregation state: 3D ARRAY / Reconstruction method: CRYSTALLOGRAPHY

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Sample preparation

ComponentName: Xylanase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.021035 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Trichoderma reesei
Buffer solutionpH: 9
Buffer component
IDConc.UnitsNameFormulaBuffer ID
10.3Msodium iodideNaI1
21.25Mammonium sulfateNH4SO41
3100mMbicine1
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: 588 / Number of grids imaged: 1 / Number of real images: 588
Image scansSampling size: 0.0311999992 microns / Dimension width: 2048 / Dimension height: 2048
EM diffractionCamera length: 1750 mm
EM diffraction shellFourier space coverage: 74.9 / High resolution: 2.3 Å / Low resolution: 2.63 Å / Multiplicity: 3.8 / Number of structure factors: 2285 / Phase residual: 53.8 deg.
EM diffraction statsFourier space coverage: 66.6 / High resolution: 1.9 Å / Number of intensities measured: 38699 / Number of structure factors: 10664 / Overall phase error: 29.95 deg. / Overall phase residual: 44.49 deg. / Phase error rejection criteria: 0 / R merge: 0.428 / R sym: 0.428
ReflectionD resolution high: 1.9 Å / D resolution low: 25.55 Å / 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
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 2dfb1
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: 49.1 Å / Length b: 59.02 Å / Length c: 7 Å / Space group name: P 21 21 21 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 2.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 2DFB
Pdb chain ID: A / Pdb chain residue range: 1-190
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 Å / Solvent vdw probe radii: 1.11 Å / 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 Å / Lowest resolution: 25.549 Å / 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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