» Articles » PMID: 10089316

Automated MAD and MIR Structure Solution

Overview
Specialty Chemistry
Date 1999 Mar 25
PMID 10089316
Citations 1285
Authors
Affiliations
Soon will be listed here.
Abstract

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

Citing Articles

Macromolecular crystallography at SPring-8 and SACLA.

Yamamoto M, Kumasaka T J Synchrotron Radiat. 2025; 32(Pt 2):304-314.

PMID: 39964789 PMC: 11892910. DOI: 10.1107/S1600577525000657.


Substrate binding and catalytic mechanism of UDP-α-D-galactofuranose: β-galactofuranoside β-(1→5)-galactofuranosyltransferase GfsA.

Oka T, Okuno A, Hira D, Teramoto T, Chihara Y, Hirata R PNAS Nexus. 2024; 3(11):pgae482.

PMID: 39507050 PMC: 11538602. DOI: 10.1093/pnasnexus/pgae482.


Sensitive Detection of Structural Differences using a Statistical Framework for Comparative Crystallography.

Hekstra D, Wang H, Klureza M, Greisman J, Dalton K bioRxiv. 2024; .

PMID: 39091831 PMC: 11291090. DOI: 10.1101/2024.07.22.604476.


A modified phase-retrieval algorithm to facilitate automatic de novo macromolecular structure determination in single-wavelength anomalous diffraction.

Fu X, Geng Z, Jiao Z, Ding W IUCrJ. 2024; 11(Pt 4):587-601.

PMID: 38904547 PMC: 11220887. DOI: 10.1107/S2052252524004846.


Structural Studies of a Complex of a CAG/CTG Repeat Sequence-Specific Binding Molecule and A-A-Mismatch-Containing DNA.

Abe K, Hirose Y, Kumagai T, Hashiya K, Hidaka K, Emura T JACS Au. 2024; 4(5):1801-1810.

PMID: 38818057 PMC: 11134352. DOI: 10.1021/jacsau.3c00830.


References
1.
Ke H . [25] Overview of isomorphous replacement phasing. Methods Enzymol. 1997; 276:448-461. DOI: 10.1016/S0076-6879(97)76071-3. View

2.
Terwilliger T . MAD phasing: Bayesian estimates of F(A). Acta Crystallogr D Biol Crystallogr. 1994; 50(Pt 1):11-6. DOI: 10.1107/S0907444993008224. View

3.
Furey W, Swaminathan S . PHASES-95: a program package for processing and analyzing diffraction data from macromolecules. Methods Enzymol. 1997; 277:590-620. DOI: 10.1016/s0076-6879(97)77033-2. View

4.
Shapiro L, Lima C . The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science. Structure. 1998; 6(3):265-7. DOI: 10.1016/s0969-2126(98)00030-6. View

5.
Pennisi E . Taking a structured approach to understanding proteins. Science. 1998; 279(5353):978-9. DOI: 10.1126/science.279.5353.978. View