+Open data
-Basic information
Entry | Database: PDB / ID: 5mjg | ||||||
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Title | Single-shot pink beam serial crystallography: Thaumatin | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / Thaumatin / Serial Crystallography / Pink beam | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Meents, A. / Oberthuer, D. / Lieske, J. / Srajer, V. | ||||||
Citation | Journal: To Be Published Title: Single-shot pink beam serial crystallography: Thaumatin Authors: Meents, A. / Oberthuer, D. / Lieske, J. / Srajer, V. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mjg.cif.gz | 150.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mjg.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mjg_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 5mjg_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 5mjg_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5mjg_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mjg ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mjg | HTTPS FTP |
-Related structure data
Related structure data | 1kwn 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: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 |
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#2: Chemical | ChemComp-SRT / |
#3: Chemical | ChemComp-NA / |
#4: 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: 2.92 Å3/Da / Density % sol: 57.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium Tartrate |
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.1-1.3 | |||||||||
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Jul 10, 2016 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.98→30 Å / Num. obs: 6850 / % possible obs: 36.6 % / Observed criterion σ(F): 3 / Redundancy: 1 % / Biso Wilson estimate: 8.04 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 38.2 | |||||||||
Reflection shell | Resolution: 2.1→2.2 Å / Num. measured obs: 3728 / Num. unique all: 245 / % possible all: 12.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KWN 1kwn Resolution: 2.1→14.98 Å / SU ML: 0.167403583403 / Cross valid method: FREE R-VALUE / σ(F): 0.316734975762 / Phase error: 13.7032148611
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3601988224 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→14.98 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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