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- PDB-7r34: Difference-refined structure of fatty acid photodecarboxylase 900... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r34 | ||||||
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Title | Difference-refined structure of fatty acid photodecarboxylase 900 ps following 400-nm laser irradiation of the dark-state determined by SFX | ||||||
![]() | Fatty acid photodecarboxylase, chloroplastic![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hadjidemetriou, K. / Coquelle, N. / Barends, T.R.M. / De Zitter, E. / Schlichting, I. / Colletier, J.P. / Weik, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned. Authors: Hadjidemetriou, K. / Coquelle, N. / Barends, T.R.M. / De Zitter, E. / Schlichting, I. / Colletier, J.P. / Weik, 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 | ![]() | 242.7 KB | Display | ![]() |
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PDB format | ![]() | 190.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7r33C ![]() 7r35C ![]() 7r36C ![]() 6zh7S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() Details: https://cxidb.org/data/177/FAP_900ps/ and https://cxidb.org/id-177.html |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 61116.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: A0A248QE08, ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-STE / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.53 % |
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Crystal grow![]() | Temperature: 281.15 K / Method: batch mode / pH: 5.5 Details: 19% (w/v) PEG 4000, 0.1 M sodium citrate pH 5.5, 10 mM spermidine |
-Data collection
Diffraction | Mean temperature: 277.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→25 Å / Num. obs: 93064 / % possible obs: 100 % / Redundancy: 270 % / CC1/2: 0.994 / R split: 0.18 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 179 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6086 / CC star: 0.797 / R split: 0.8 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6ZH7 Resolution: 2→10 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.71 / Phase error: 46.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.65 Å2 / Biso mean: 34.4324 Å2 / Biso min: 6.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→10 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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