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Yorodumi- PDB-5p28: Automated refinement of diffraction data obtained from an endothi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5p28 | ||||||
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Title | Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 126 | ||||||
Components | endothiapepsin | ||||||
Keywords | HYDROLASE / fragment screening / method development / aspartic protease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.345 Å | ||||||
Model details | All 364 structures of this series were generated by an automated refinement pipeline and, thus, not ...All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments are missing in the structural model even when present as indicated by the electron density) | ||||||
Authors | Schiebel, J. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Structure / Year: 2016 Title: High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits. Authors: Schiebel, J. / Krimmer, S.G. / Rower, K. / Knorlein, A. / Wang, X. / Park, A.Y. / Stieler, M. / Ehrmann, F.R. / Fu, K. / Radeva, N. / Krug, M. / Huschmann, F.U. / Glockner, S. / Weiss, M.S. ...Authors: Schiebel, J. / Krimmer, S.G. / Rower, K. / Knorlein, A. / Wang, X. / Park, A.Y. / Stieler, M. / Ehrmann, F.R. / Fu, K. / Radeva, N. / Krug, M. / Huschmann, F.U. / Glockner, S. / Weiss, M.S. / Mueller, U. / Klebe, G. / Heine, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5p28.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5p28.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 5p28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/5p28 ftp://data.pdbj.org/pub/pdb/validation_reports/p2/5p28 | HTTPS FTP |
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-Group deposition
ID | G_1002001 (364 entries) |
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Title | High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits. |
Type | undefined |
Description | High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits. |
-Related structure data
Related structure data | 4y5lS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 126 with the SMILES code O=C(CC1=CC=CC=C1)NN1CCCCC1 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.34→42.758 Å / Num. obs: 70909 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.059 % / Biso Wilson estimate: 8.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.11 / Χ2: 0.946 / Net I/σ(I): 11.14 / Num. measured all: 287870 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y5L Resolution: 1.345→39.587 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 17.05 / Stereochemistry target values: ML Details: All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments ...Details: All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments are missing in the structural model even when present as indicated by the electron density)
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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: 38.08 Å2 / Biso mean: 11.6439 Å2 / Biso min: 4.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.345→39.587 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
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