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- PDB-7h5u: Crystal structure of endothiapepsin PF_cryo3 in complex with JFD0... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7h5u | |||||||||
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Title | Crystal structure of endothiapepsin PF_cryo3 in complex with JFD03909 at 100 K | |||||||||
![]() | Endothiapepsin | |||||||||
![]() | HYDROLASE / Endopeptidase / room temperature | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Huang, C.-Y. / Aumonier, S. / Olieric, V. / Wang, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryocooled crystals. Authors: Huang, C.Y. / Aumonier, S. / Olieric, V. / Wang, 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 | ![]() | 80.7 KB | Display | ![]() |
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PDB format | ![]() | 60.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.2 KB | Display | ![]() |
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Full document | ![]() | 449.4 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Group deposition
ID | G_1002290 (30 entries) |
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Title | A High-Throughput Method for Room-Temperature Macromolecular Crystallography from Frozen Crystals |
Type | undefined |
Description | A High-Throughput Method for Room-Temperature Macromolecular Crystallography from Frozen Crystals |
-Related structure data
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: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P11838, endothiapepsin | ||||
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#2: Chemical | ChemComp-DMS / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M ammonium acetate, 0.1 M sodium acetate pH 4.6, and 26 - 30% (v/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→49.26 Å / Num. obs: 21848 / % possible obs: 99.6 % / Biso Wilson estimate: 35.46 Å2 / Rmerge F all: 0.15 / CC1/2: 0.99 / Net I/σ(I): 9.51 |
Reflection shell | Resolution: 1.99→2.08 Å / Redundancy: 7.15 % / Rmerge F all: 1.13 / Num. unique obs: 3496 / CC1/2: 0.65 / Net I/σ(I) all: 1.46 / % possible all: 99.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso max: 146.6 Å2 / Biso mean: 38.01 Å2 / Biso min: 20 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.99→21.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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