sbgrid-phenix2016-data

SBGrid PHENIX 2016

Looking forward to seeing you at PHENIX 2016.

We will be using PHENIX during the workshop but you may also want to install PyMOL, CCP4 (includes COOT) and/ any other tools you prefer to use. https://sbgrid.org/wiki/client_install

Reference Datasets

We have assembled a set of reference data for discussion during workshop.

You can download that data here : Workshop2016Datasets.tar.bz2 - 37.5Mb

Directory names

• kd : processing results from Kay Diederichs
• sbdb : automated data reduction results
• PDB CODE.fasta : sequence file from RCSB

See Archive directory structure below.

Images are not necessary but can be downloaded from the SBDB with:

rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/<dataset number>  .

Dataset info

Each dataset includes a readme.txt file with a description.

Dataset #3 : X-Ray Diffraction data from Lin28/let-7d microRNA complex, source of 3TRZ structure

Zn-SAD dataset

Dataset #97 : X-Ray Diffraction data from Thermoanaerobacter tengcongensis SONO (H-NOX) in complex with dioxygen, source of 1XBN structure

This is a three wavelength MAD data collected at the iron edge. E1 = 7134.03 eV; E2 = 7634 eV; E3 = 7124.35 eV.

Dataset #111 : X-Ray Diffraction data from 'Spinach' RNA-chromophore complex, source of 4TS0 structure

Dataset #123 : X-Ray Diffraction data from HSV-2 gH/gL complex, source of 3M1C structure

This is a selenomethionine single-wavelength anomalous diffraction data set collected at 0.9789 angstrom wavelength

Archive directory structure

├── 111
│   ├── 4TSO.fasta
│   ├── kd
│   │   ├── CORRECT.LP
│   │   ├── XDS_ASCII.HKL
│   │   └── XDS.INP
│   ├── readme.txt
│   └── sbdb
│       ├── proc-0.mtz
│       ├── proc-1.mtz
│       ├── proc-2.mtz
│       └── proc-3.mtz
├── 123
│   ├── 3M1C.fasta
│   ├── kd
│   │   ├── CORRECT.LP
│   │   ├── XDS_ASCII.HKL
│   │   └── XDS.INP
│   ├── readme.txt
│   └── sbdb
│       ├── proc-0.mtz
│       ├── proc-1.mtz
│       ├── proc-2.mtz
│       └── proc-3.mtz
├── 3
│   ├── 3TRZ.fasta
│   ├── kd
│   │   ├── CORRECT.LP
│   │   ├── XDS_ASCII.HKL
│   │   └── XDS.INP
│   ├── readme.txt
│   └── sbdb
│       ├── proc-1.mtz
│       ├── proc-2.mtz
│       └── proc-3.mtz
└── 97
    ├── 1XBN.fasta
    ├── readme.txt
    └── sbdb
        ├── proc-1.mtz
        └── proc-2.mtz