6NCT

Structure of p110alpha/niSH2 - vector data collection


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II.

Miller, M.S.Maheshwari, S.Shi, W.Gao, Y.Chu, N.Soares, A.S.Cole, P.A.Amzel, L.M.Fuchs, M.R.Jakoncic, J.Gabelli, S.B.

(2019) Molecules 24: --

  • DOI: 10.3390/molecules24030496
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Advances in synchrotron technology are changing the landscape of macromolecular crystallography. The two recently opened beamlines at NSLS-II-AMX and FMX-deliver high-flux microfocus beams that open new possibilities for crystallographic data collect ...

    Advances in synchrotron technology are changing the landscape of macromolecular crystallography. The two recently opened beamlines at NSLS-II-AMX and FMX-deliver high-flux microfocus beams that open new possibilities for crystallographic data collection. They are equipped with state-of-the-art experimental stations and automation to allow data collection on previously intractable crystals. Optimized data collection strategies allow users to tailor crystal positioning to optimally distribute the X-ray dose over its volume. Vector data collection allows the user to define a linear trajectory along a well diffracting volume of the crystal and perform rotational data collection while moving along the vector. This is particularly well suited to long, thin crystals. We describe vector data collection of three proteins-Akt1, PI3Kα, and CDP-Chase-to demonstrate its application and utility. For smaller crystals, we describe two methods for multicrystal data collection in a single loop, either manually selecting multiple centers (using H108A-PHM as an example), or "raster-collect", a more automated approach for a larger number of crystals (using CDP-Chase as an example).


    Organizational Affiliation

    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. gabelli@jhmi.edu.,Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. yuangao@bnl.gov.,Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA. pacole@bwh.harvard.edu.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. sweta@jhmi.edu.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. gabelli@jhmi.edu.,Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. mfuchs@bnl.gov.,Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. jjakoncic@bnl.gov.,Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA. nchu3@bwh.harvard.edu.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. gabelli@jhmi.edu.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. mamzel@jhmi.edu.,Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. soares@bnl.gov.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. michelle.miller@jhmi.edu.,Case Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, OH 44106, USA. wushi@bnl.gov.,Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA. wushi@bnl.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
A
1096Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: 2.7.1.153
Find proteins for P42336 (Homo sapiens)
Go to Gene View: PIK3CA
Go to UniProtKB:  P42336
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha
B
279Homo sapiensMutation(s): 0 
Gene Names: PIK3R1 (GRB1)
Find proteins for P27986 (Homo sapiens)
Go to Gene View: PIK3R1
Go to UniProtKB:  P27986
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
144
Query on 144

Download SDF File 
Download CCD File 
A, B
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 115.355α = 90.00
b = 117.724β = 90.00
c = 151.331γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA062924

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Database references
  • Version 1.2: 2019-12-04
    Type: Author supporting evidence