Automated MAD and MIR structure solution

By T. C. Terwilliger, J. Berendzen. 1999

A fully automated procedure for solving MIR and MAD structures has been developed using a scoring scheme to convert the structure-solution process into an optimization problem.

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, neutral): “D75, 861–877 Liebschner et al. Recent developments in Phenix 865 3 MAD, multiple-wavelength anomalous diffraction; MIR, multiple isomorphous replacement; SIR, single isomorphous replacement. ture Search; Grosse-Kunstleve & Adams, 2003; Bunkóczi et al., 2013), SOLVE (Terwilliger & Berendzen, 1999), ”
Phaser crystallographic software (2007, methodology): “To facilitate this, Phaser runs the refinement and substructure completion in both hands [as does other experimental phasing software, e.g. Solve (Terwilliger & Berendzen, 1999) and autosharp (Vonrhein et al., 2006)].”
BALBES: a molecular-replacement pipeline (2007, methodology): “The application of information derived from the PDB for molecular replacement, phase improvement (Terwilliger & Berendzen, 1999) and model building (Emsley & Cowtan, 2004; Jones et al., 1991) now routinely takes place.”
Structural basis of the α1–β subunit interaction of voltage-gated Ca2+ channels (2004, methodology): “Structure determination and refinement The locations of Se atoms in the β 3 core crystal were determined with the program SOLV”
Replication by human DNA polymerase-ι occurs by Hoogsteen base-pairing (2004, methodology): “We found the positions of nine selenium atoms from the SeMet data using the program SOLV”
High-throughput crystallography for lead discovery in drug design (2002, unknown): “New approaches have provided fully automated phasin”
Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. (2009, unknown): “3 (Otwinowski and Minor, 1997) and Se atom positions were determined and phases were obtained using SOLVE (Terwilliger and Berendzen, 1999).”
Structure of a glutamate transporter homologue from Pyrococcus horikoshii (2004, methodology): “For the Pt MAD data set, initial heavy atom sites were found using Solv”
Crystal structure of chondroitin polymerase from Escherichia coli K4. (2009, methodology): “The phases were improved using solvent-flipping and ncs averaging (based on selenium sites) with Resolve [9].”
The closed structure of presequence protease PreP forms a unique 10 000 Å3 chamber for proteolysis (2006, methodology): “All 40 selenium atoms in the asymmetric unit were located by SHELXD (Schneider and Sheldrick, 2002) and phases were calculated and improved first with MLPHARE (Otwinowski, 1991) to confirm the solution and then with SOLVE (Terwilliger and Berendzen, 1999) and RESOLVE (Terwilliger, 2000) to create th”
Activation of a vinculin‐binding site in the talin rod involves rearrangement of a five‐helix bundle (2004, methodology): “The sites of selenium and platinum atoms were determined using SOLVE (Terwilliger and Berendzen, 1999).”
Crystal structure and mechanism of a calcium-gated potassium channel (2002, methodology): “Heavy atom positions for a first derivative were determined by Patterson search using SOLV”
Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family. (2010, methodology): “Density modification and automatic tracing of ∼64% of the amino acids were performed with RESOLVE (FOM = 0.80).”