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- PDB-5k7r: MicroED structure of trypsin at 1.7 A resolution -

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Entry
Database: PDB / ID: 5k7r
TitleMicroED structure of trypsin at 1.7 A resolution
DescriptorCationic trypsin (E.C.3.4.21.4)
KeywordsHYDROLASE / Hydrolase
Specimen sourceBos taurus / mammal / Bovine / ウシ /
MethodElectron crystallography (1.7 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: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4043
Polyers23,3241
Non-polymers802
Water3,513195
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (A2)170
ΔGint (kcal/M)-21
Surface area (A2)8620
MethodPISA
Unit cell
gamma
alpha
beta
Length a, b, c (A): 53.184, 56.428, 64.672 / Angle α, β, γ (deg.): 90.00, 90.00, 90.00

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Components

#1: Polypeptide(L)Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: P00760, EC: 3.4.21.4
#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.: 195 / 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: Trypsin / Type: ORGANELLE OR CELLULAR COMPONENT
VitrificationCryogen name: ETHANE

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Data collection

MicroscopyMicroscope model: FEI TECNAI F20 / Date: Mar 11, 2016
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: 27.63 A / Number all: 145833 / Number obs: 23542 / Rmerge I obs: 0.773 / Rpim I all: 0.332 / NetI over sigmaI: 2.3 / Redundancy: 6.2 / Percent possible obs: 73.8
Reflection shell
Rmerge I obsHighest resolutionLowest resolutionNumber unique allNumber unique obsRpim I allNetI over sigmaI obsRedundancyPercent possible all
3.6321.501.534022813.2400.31.418.2
0.2108.2227.6316092170.0787.67.494.2

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Processing

SoftwareName: PHENIX / Version: (1.10_2155: ???) / Classification: refinement
ComputingStructure refinement: PHENIX (1.10_2155: ???)
3D reconstructionResolution: 1.7 A / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Atomic model buildingRef protocol: OTHER / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 2PTN
Pdb chain id: A
RefineOverall SU ML: 0.33 / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 28.86
Solvent computationSolvent shrinkage radii: 0.9 A / Solvent vdw probe radii: 1.11 A
Least-squares processR factor R free: 0.2811 / R factor R work: 0.2479 / R factor obs: 0.2495 / Highest resolution: 1.7 A / Lowest resolution: 25.86 A / Number reflection R free: 919 / Number reflection obs: 19277 / Percent reflection R free: 4.77 / Percent reflection obs: 87.5
Refine LS restraints
Refine idTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0051666
ELECTRON CRYSTALLOGRAPHYf_angle_d0.7392264
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d12.1151000
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.049254
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.004289
Refine LS shell

Refine id: ELECTRON CRYSTALLOGRAPHY

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.70010.42370.38721.789769166856.00
1.78970.43460.36211.9018111226176.00
1.90180.36060.31652.0486126267190.00
2.04860.33860.26912.2546141288497.00
2.25460.27150.24292.5806168289397.00
2.58060.23520.21543.2503173291697.00
3.25030.18040.166425.8634131306597.00

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