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- PDB-6sro: X-ray pump X-ray probe on thaumatin nanocrystals: 76 fs time delay -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sro | ||||||
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Title | X-ray pump X-ray probe on thaumatin nanocrystals: 76 fs time delay | ||||||
![]() | Thaumatin-1 | ||||||
![]() | PLANT PROTEIN / Radiation damage / SERIAL femtosecond CRYSTALLOGRAPHY / X-ray FREE-ELECTRON LASER / time-resolved crystallography | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kloos, M. / Gorel, A. / Nass, K. | ||||||
![]() | ![]() Title: Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Authors: Nass, K. / Gorel, A. / Abdullah, M.M. / V Martin, A. / Kloos, M. / Marinelli, A. / Aquila, A. / Barends, T.R.M. / Decker, F.J. / Bruce Doak, R. / Foucar, L. / Hartmann, E. / Hilpert, M. / ...Authors: Nass, K. / Gorel, A. / Abdullah, M.M. / V Martin, A. / Kloos, M. / Marinelli, A. / Aquila, A. / Barends, T.R.M. / Decker, F.J. / Bruce Doak, R. / Foucar, L. / Hartmann, E. / Hilpert, M. / Hunter, M.S. / Jurek, Z. / Koglin, J.E. / Kozlov, A. / Lutman, A.A. / Kovacs, G.N. / Roome, C.M. / Shoeman, R.L. / Santra, R. / Quiney, H.M. / Ziaja, B. / Boutet, S. / Schlichting, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.3 KB | Display | ![]() |
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PDB format | ![]() | 39.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6sr0C ![]() 6sr1C ![]() 6sr2C ![]() 6sr3C ![]() 6sr4C ![]() 6sr5C ![]() 6srjC ![]() 6srkC ![]() 6srlC ![]() 6srpC ![]() 6srqC ![]() 5fgtS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % / Description: nanocrystals |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7 / Details: 0.8 M NA, K TARTRATE, 0.1 M NA HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.75 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→23 Å / Num. obs: 11104 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.979 / R split: 0.094 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.32→2.36 Å / Mean I/σ(I) obs: 4.2 / Num. unique obs: 850 / CC1/2: 0.965 / R split: 0.312 |
Serial crystallography measurement | Focal spot size: 0.025 µm2 / Pulse duration: 15 fsec. / Pulse energy: 500 µJ / Pulse photon energy: 7.07 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Description: GDVN injection / Method: injection |
Serial crystallography data reduction | Frames indexed: 11000 / Lattices indexed: 11000 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5fgt Resolution: 2.3→23 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.198 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.162 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The submitted coordinates represent the mean of 100 coordinate sets obtained by refining against 100 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The submitted coordinates represent the mean of 100 coordinate sets obtained by refining against 100 different integrated diffraction intensity datasets obtained by jackknife resampling of the diffraction snapshots. The coordinate header originates from one of the individual refinements. Cysteine residues were modeled as alanines and non-covalently attached sulphur atoms.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.27 Å2 / Biso mean: 31.222 Å2 / Biso min: 16.89 Å2
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Refinement step | Cycle: final / Resolution: 2.3→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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