5FXN

Structure of thermolysin solved by SAD from data collected by Direct Data Collection (DDC) using the ESRF RoboDiff goniometer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Robodiff: Combining a Sample Changer and Goniometer for Highly Automated Macromolecular Crystallography Experiments.

Nurizzo, D.Bowler, M.W.Caserotto, H.Dobias, F.Giraud, T.Surr, J.Guichard, N.Papp, G.Guijarro, M.Mueller-Dieckmann, C.Flot, D.Mcsweeney, S.Cipriani, F.Theveneau, P.Leonard, G.A.

(2016) Acta Crystallogr.,Sect.D 72: 966

  • DOI: 10.1107/S205979831601158X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, ...

    Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically.


    Organizational Affiliation

    European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMOLYSIN
A
315Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

Download SDF File 
Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
VAL
Query on VAL

Download SDF File 
Download CCD File 
A
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.144 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.100α = 90.00
b = 93.100β = 90.00
c = 130.302γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
SHELXDEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection, Refinement description
  • Version 2.0: 2018-06-20
    Type: Advisory, Atomic model, Data collection, Derived calculations