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Open data
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Basic information
Entry | Database: PDB / ID: 7qlo | ||||||
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Title | rsKiiro pump dump probe structure by TR-SFX | ||||||
![]() | rsKiiro | ||||||
![]() | FLUORESCENT PROTEIN / rsKiiro / Green to red photoconvertible GFP-like protein EosFP | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green to red photoconvertible GFP-like protein EosFP![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Thor, J.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Optical control of ultrafast structural dynamics in a fluorescent protein. Authors: Hutchison, C.D.M. / Baxter, J.M. / Fitzpatrick, A. / Dorlhiac, G. / Fadini, A. / Perrett, S. / Maghlaoui, K. / Lefevre, S.B. / Cordon-Preciado, V. / Ferreira, J.L. / Chukhutsina, V.U. / ...Authors: Hutchison, C.D.M. / Baxter, J.M. / Fitzpatrick, A. / Dorlhiac, G. / Fadini, A. / Perrett, S. / Maghlaoui, K. / Lefevre, S.B. / Cordon-Preciado, V. / Ferreira, J.L. / Chukhutsina, V.U. / Garratt, D. / Barnard, J. / Galinis, G. / Glencross, F. / Morgan, R.M. / Stockton, S. / Taylor, B. / Yuan, L. / Romei, M.G. / Lin, C.Y. / Marangos, J.P. / Schmidt, M. / Chatrchyan, V. / Buckup, T. / Morozov, D. / Park, J. / Park, S. / Eom, I. / Kim, M. / Jang, D. / Choi, H. / Hyun, H. / Park, G. / Nango, E. / Tanaka, R. / Owada, S. / Tono, K. / DePonte, D.P. / Carbajo, S. / Seaberg, M. / Aquila, A. / Boutet, S. / Barty, A. / Iwata, S. / Boxer, S.G. / Groenhof, G. / van Thor, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.3 KB | Display | ![]() |
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PDB format | ![]() | 46.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7qliC ![]() 7qljC ![]() 7qlkC ![]() 7qllC ![]() 7qlmC ![]() 7qlnC ![]() 5oqeS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 25152.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.94 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 0.2 M LITHIUM SULFATE 0.1 M TRIS-CL PH 8.5 23-30% PEG 3350 |
-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 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.305 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→19 Å / Num. obs: 51252 / % possible obs: 100 % / Redundancy: 157 % / Biso Wilson estimate: 19.87 Å2 / CC1/2: 0.99 / R split: 0.1219 / Net I/σ(I): 4.566 |
Reflection shell | Resolution: 1.31→1.34 Å / Num. unique obs: 172 / CC1/2: 0.05 / R split: 3.5 |
Serial crystallography measurement | Focal spot size: 1 µm2 / Pulse duration: 4 fsec. / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OQE Resolution: 1.31→11.99 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.856 / SU B: 6.525 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The model corresponds to 21 percentage of non-extrapolated structure factors.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.329 Å2
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Refinement step | Cycle: 1 / Resolution: 1.31→11.99 Å
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Refine LS restraints |
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