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- PDB-6clk: 1.01 A MicroED structure of GSNQNNF at 0.82 e- / A^2 -

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Entry
Database: PDB / ID: 6clk
Title1.01 A MicroED structure of GSNQNNF at 0.82 e- / A^2
ComponentsGSNQNNF
KeywordsPROTEIN FIBRIL / Amyloid fibril / prion / zinc binding
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.01 Å
AuthorsHattne, J. / Shi, D. / Glynn, C. / Zee, C.-T. / Gallagher-Jones, M. / Martynowycz, M.W. / Rodriguez, J.A. / Gonen, T.
CitationJournal: Structure / Year: 2018
Title: Analysis of Global and Site-Specific Radiation Damage in Cryo-EM.
Authors: Johan Hattne / Dan Shi / Calina Glynn / Chih-Te Zee / Marcus Gallagher-Jones / Michael W Martynowycz / Jose A Rodriguez / Tamir Gonen /
Abstract: Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron ...Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.
History
DepositionMar 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: GSNQNNF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9043
Polymers7801
Non-polymers1242
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-15 kcal/mol
Surface area1190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)4.840, 14.100, 17.380
Angle α, β, γ (deg.)83.65, 85.53, 82.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide GSNQNNF


Mass: 779.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Synthetic proto-filament / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.000899141 MDa / Experimental value: NO
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
10.1 MMESC6H13NO4S1
210 %MPDC6H14O21
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 30 %

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 2.1 sec. / Electron dose: 0.00357 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 826 / Num. of grids imaged: 1 / Num. of real images: 826
Image scansSampling size: 31.2 µm / Width: 2048 / Height: 2048
EM diffractionCamera length: 730 mm
EM diffraction shellResolution: 1.01→1.04 Å / Fourier space coverage: 77.99 % / Multiplicity: 4.3 / Num. of structure factors: 124 / Phase residual: 62.42 °
EM diffraction statsFourier space coverage: 80 % / High resolution: 1.01 Å / Num. of intensities measured: 12579 / Num. of structure factors: 1952 / Phase error: 42.71 ° / Phase residual: 42.71 ° / Phase error rejection criteria: 0 / Rmerge: 0.289 / Rsym: 0.289
DetectorDate: Aug 1, 2017

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Processing

Software
NameVersionClassification
REFMAC5.8.0194refinement
XDSdata reduction
XSCALEdata scaling
EM software
IDNameVersionCategory
1EM-Menu4.0.9.75image acquisition
8REFMAC5.8.0194model refinement
EM 3D crystal entity∠α: 83.65 ° / ∠β: 85.53 ° / ∠γ: 82.814 ° / A: 4.84 Å / B: 14.1 Å / C: 17.38 Å / Space group name: P1 / Space group num: 1
CTF correctionType: NONE
3D reconstructionResolution: 1.01 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 4.322 / Protocol: OTHER / Space: RECIPROCAL / Details: Electron scattering factors
RefinementResolution: 1.01→13.92 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.884 / SU B: 1.01 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26736 167 8.8 %RANDOM
Rwork0.2605 ---
obs0.26111 1721 80.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 4.322 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.15 Å20.03 Å2
2---0.29 Å2-0.43 Å2
3---0.98 Å2
Refinement stepCycle: 1 / Total: 63
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0240.0258
ELECTRON CRYSTALLOGRAPHYr_bond_other_d00.0239
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.6861.88676
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg1.046392
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg5.32656
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg62.321285
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg6.657157
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_4_deg
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0510.26
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0120.0273
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other00.0211
ELECTRON CRYSTALLOGRAPHYr_nbd_refined
ELECTRON CRYSTALLOGRAPHYr_nbd_other
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined
ELECTRON CRYSTALLOGRAPHYr_nbtor_other
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_other
ELECTRON CRYSTALLOGRAPHYr_metal_ion_refined
ELECTRON CRYSTALLOGRAPHYr_metal_ion_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_vdw_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_vdw_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_hbond_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_hbond_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_metal_ion_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_metal_ion_other
ELECTRON CRYSTALLOGRAPHYr_mcbond_it0.3990.40628
ELECTRON CRYSTALLOGRAPHYr_mcbond_other0.3750.38526
ELECTRON CRYSTALLOGRAPHYr_mcangle_it0.6750.57730
ELECTRON CRYSTALLOGRAPHYr_mcangle_other0.6740.58131
ELECTRON CRYSTALLOGRAPHYr_scbond_it0.430.43330
ELECTRON CRYSTALLOGRAPHYr_scbond_other0.4230.44531
ELECTRON CRYSTALLOGRAPHYr_scangle_it
ELECTRON CRYSTALLOGRAPHYr_scangle_other0.6310.65642
ELECTRON CRYSTALLOGRAPHYr_long_range_B_refined3.4255.03650
ELECTRON CRYSTALLOGRAPHYr_long_range_B_other3.0624.79650
ELECTRON CRYSTALLOGRAPHYr_rigid_bond_restr
ELECTRON CRYSTALLOGRAPHYr_sphericity_free
ELECTRON CRYSTALLOGRAPHYr_sphericity_bonded
LS refinement shellResolution: 1.013→1.039 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 11 -
Rwork0.374 113 -
obs--77.99 %

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