1E6F

Human MIR-receptor, repeat 11

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.273 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Locating the Anomalous Scatterer Substructures in Halide and Sulfur Phasing

Uson, I., Schmidt, B., Von Buelow, R., Grimme, S., Von Figura, K., Dauter, M., Rajashankar, K.R., Dauter, Z., Sheldrick, G.M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 57

  • DOI: 10.1107/s090744490201884x
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Improved data quality now makes it feasible to exploit the weak anomalous signal derived only from the sulfurs inherent to the protein or in particular from halide ions incorporated by soaking. The latter technique requires the location of a high num ...

    Improved data quality now makes it feasible to exploit the weak anomalous signal derived only from the sulfurs inherent to the protein or in particular from halide ions incorporated by soaking. The latter technique requires the location of a high number of partially occupied halide sites. This number appears to be roughly proportional to the exposed protein surface. This paper explores the application of dual-space ab initio methods as implemented in the program SHELXD to the location of substructures of sulfur in SAD experiments, bromide in SAD and MAD experiments and iodide using SAD and SIRAS to determine the anomalous-atom substructure. Sets of atoms consistent with the Patterson function were generated as a starting point for the dual-space recycling procedure in SHELXD. The substructure is then expanded to the full structure by maximum-likelihood phasing with SHARP and density modification with the program DM. Success in the location of the substructures and subsequent phasing depends critically on the quality of the data and on the extent of the anomalous signal. This varies with each crystal and soak, but for the same crystal the significance of the anomalous signal was found to be highly sensitive to the redundancy of the intensity measurements, which in some cases made all the difference. This is illustrated by the determination of the previously unknown structure of repeat 11 of the human mannose-6-phosphate/insulin-like growth factor II receptor (Man6P/IGFII-receptor), with 310 amino acids in the asymmetric unit, which was phased by soaking the crystals in a cryoprotectant solution containing halide anions.

    Organizational Affiliation: 

    Lehrstuhl für Strukturchemie, Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany. uson@shelx.uni-ac.gwdg.de



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTORA, B143Homo sapiensMutation(s): 0 
Gene Names: IGF2R, MPRI
Find proteins for P11717 (Homo sapiens)
Explore P11717 
Go to UniProtKB:  P11717
NIH Common Fund Data Resources
PHAROS  P11717
GTEx  ENSG00000197081
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.273 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.5α = 90
b = 49β = 90
c = 120.4γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-07-24
    Changes: Data collection