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- PDB-4wla: Time Resolved Serial Femtosecond Crystallography Captures High Re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wla | ||||||
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Title | Time Resolved Serial Femtosecond Crystallography Captures High Resolution Intermediates of PYP | ||||||
![]() | Photoactive yellow protein | ||||||
![]() | SIGNALING PROTEIN / Bluelight photoreceptor / time-resolved serial femtosecond crystallography / nanocrystals / microcrystals | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tenboer, J. / Schmidt, M. | ||||||
![]() | ![]() Title: Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Authors: Tenboer, J. / Basu, S. / Zatsepin, N. / Pande, K. / Milathianaki, D. / Frank, M. / Hunter, M. / Boutet, S. / Williams, G.J. / Koglin, J.E. / Oberthuer, D. / Heymann, M. / Kupitz, C. / ...Authors: Tenboer, J. / Basu, S. / Zatsepin, N. / Pande, K. / Milathianaki, D. / Frank, M. / Hunter, M. / Boutet, S. / Williams, G.J. / Koglin, J.E. / Oberthuer, D. / Heymann, M. / Kupitz, C. / Conrad, C. / Coe, J. / Roy-Chowdhury, S. / Weierstall, U. / James, D. / Wang, D. / Grant, T. / Barty, A. / Yefanov, O. / Scales, J. / Gati, C. / Seuring, C. / Srajer, V. / Henning, R. / Schwander, P. / Fromme, R. / Ourmazd, A. / Moffat, K. / Van Thor, J.J. / Spence, J.C. / Fromme, P. / Chapman, H.N. / Schmidt, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.9 KB | Display | ![]() |
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PDB format | ![]() | 30.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 446.9 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wl9C ![]() 2phyS S: Starting model for refinement C: citing same article ( |
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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: 13888.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.19 % / Description: Rsplit=0.092 |
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Crystal grow | Temperature: 296 K / Method: batch mode / pH: 7 Details: Microcrystals of ~2 x 2 x 5 um3 size were created by centrifugation in spin filters |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD detector / Detector: PIXEL / Date: Jun 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.36 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→16.73 Å / Num. obs: 13500 / % possible obs: 100 % / Redundancy: 1500 % / R split: 0.092 / Net I/σ(I): 8.7 |
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Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2PHY Resolution: 1.6→16.73 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.507 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.831 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→16.73 Å
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Refine LS restraints |
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