+Open data
-Basic information
Entry | Database: PDB / ID: 1luq | ||||||
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Title | Full Matrix Error Analysis of Streptavidin | ||||||
Components | Streptavidin | ||||||
Keywords | BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å | ||||||
Authors | Merritt, E.A. / Le Trong, I. | ||||||
Citation | Journal: To be Published Title: Full Matrix Error Analysis of Streptavidin Authors: Merritt, E.A. / Le Trong, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1luq.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1luq.ent.gz | 145.4 KB | Display | PDB format |
PDBx/mmJSON format | 1luq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1luq_validation.pdf.gz | 405.9 KB | Display | wwPDB validaton report |
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Full document | 1luq_full_validation.pdf.gz | 410.7 KB | Display | |
Data in XML | 1luq_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1luq_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/1luq ftp://data.pdbj.org/pub/pdb/validation_reports/lu/1luq | HTTPS FTP |
-Related structure data
Related structure data | 1df8S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13265.336 Da / Num. of mol.: 2 / Mutation: S1045A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Description: T7 expression system / Production host: Escherichia coli (E. coli) / References: GenBank: 4376079, UniProt: P22629*PLUS #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density meas: 34.8 Mg/m3 / Density % sol: 41.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: ammonium sulfate, sodium acetate, biotin, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→14 Å / Num. all: 135985 / Num. obs: 135985 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 0.96→0.97 Å / Rmerge(I) obs: 0.602 / % possible all: 45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DF8 Resolution: 0.96→14 Å / Num. parameters: 19886 / Num. restraintsaints: 25548 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4.0%. Entry 1LUQ contains the crystallographic model used for error analysis and model comparison as reported in Merritt et al. The final ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4.0%. Entry 1LUQ contains the crystallographic model used for error analysis and model comparison as reported in Merritt et al. The final crystallographic model for this structure will be deposited separately under a different accession code.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 14 / Occupancy sum hydrogen: 1667.5 / Occupancy sum non hydrogen: 2128 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.96→14 Å
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Refine LS restraints |
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