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- PDB-5k7s: MicroED structure of proteinase K at 1.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 5k7s
TitleMicroED structure of proteinase K at 1.6 A resolution
DescriptorProteinase K (E.C.3.4.21.64)
KeywordsHYDROLASE / Hydrolase
Specimen sourceEngyodontium album / fungus
MethodElectron crystallography (1.6 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: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0113
Polyers28,9311
Non-polymers802
Water3,981221
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)90
ΔGint (kcal/M)-12
Surface area (Å2)9990
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.059, 67.059, 100.713
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)Proteinase K / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28930.783 Da / Num. of mol.: 1 / Source: (natural) Engyodontium album / fungus / References: UniProt: P06873, EC: 3.4.21.64

Molecular function

#2: ChemicalChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: Proteinase K / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.028938 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Engyodontium album
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
11.2Mammonium sulfateNH4SO41
20.1MTris1
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 / Date: Mar 7, 2016
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: 295 / Number of grids imaged: 1 / Number of real images: 295
Image scansSampling size: 0.0311999992 microns / Dimension width: 2048 / Dimension height: 2048
EM diffractionCamera length: 1200 mm
EM diffraction shellFourier space coverage: 85.8 / High resolution: 1.6 Å / Low resolution: 1.64 Å / Multiplicity: 5.7 / Number of structure factors: 1857 / Phase residual: 53.1 deg.
EM diffraction statsFourier space coverage: 81.1 / High resolution: 1.3 Å / Number of intensities measured: 302892 / Number of structure factors: 46369 / Overall phase error: 24.33 deg. / Overall phase residual: 32.2 deg. / Phase error rejection criteria: 0 / R merge: 0.728 / R sym: 0.728
ReflectionD resolution high: 1.3 Å / D resolution low: 20.75 Å / Number all: 302892 / Number obs: 46369 / Rmerge I obs: 0.728 / Rpim I all: 0.295 / NetI over sigmaI: 2.4 / Redundancy: 6.5 / Percent possible obs: 81.1
Reflection shell
Rmerge I obsHighest resolutionLowest resolutionNumber unique allNumber unique obsRpim I allNetI over sigmaI obsRedundancyPercent possible all
2.4551.301.32204410051.9840.42.036.6
0.2007.1220.7527393860.0738.17.193.1

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Processing

SoftwareName: PHENIX / Version: (1.10_2155: ???) / Classification: refinement
EM software
IDNameVersionCategoryImaging IDFitting IDImage 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 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: 67.6 Å / Length b: 67.6 Å / Length c: 101.36 Å / Space group name: P 43 21 2 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 1.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 5I9S
Pdb chain ID: A / Pdb chain residue range: 1-279
RefineOverall SU ML: 0.25 / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 24.33
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.2546 / R factor R work: 0.2235 / R factor obs: 0.2255 / Highest resolution: 1.6 Å / Lowest resolution: 20.751 Å / Number reflection R free: 1936 / Number reflection obs: 29776 / Percent reflection R free: 6.5 / Percent reflection obs: 96.05
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0042070
ELECTRON CRYSTALLOGRAPHYf_angle_d0.6332814
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d9.1701214
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.043312
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.003370
Refine LS shell

Refine ID: ELECTRON CRYSTALLOGRAPHY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.60000.42250.36331.6400124173386.00
1.64000.38130.34781.6844128181890.00
1.68440.35090.32991.7339124190994.00
1.73390.32160.29811.7898132199897.00
1.78980.37080.28071.8538139198398.00
1.85380.30520.25731.9279142199798.00
1.92790.25930.24432.0156143200798.00
2.01560.26570.22342.1218143201098.00
2.12180.27240.20962.2546139201398.00
2.25460.25380.21652.4284146201898.00
2.42840.22430.21312.6723140203498.00
2.67230.24180.19953.0580142206698.00
3.05800.16530.15453.8487142208198.00
3.84870.16330.150920.7528152217397.00

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