Maximum-likelihood density modification
TL;DR: A likelihood-based density modification approach is developed that can incorporate expected electron-density information from a wide variety of sources.
read more
Abstract: A likelihood-based approach to density modification is developed that can be applied to a wide variety of cases where some information about the electron density at various points in the unit cell is available. The key to the approach consists of developing likelihood functions that represent the probability that a particular value of electron density is consistent with prior expectations for the electron density at that point in the unit cell. These likelihood functions are then combined with likelihood functions based on experimental observations and with others containing any prior knowledge about structure factors to form a combined likelihood function for each structure factor. A simple and general approach to maximizing the combined likelihood function is developed. It is found that this likelihood-based approach yields greater phase improvement in model and real test cases than either conventional solvent flattening and histogram matching or a recent reciprocal-space solvent-flattening procedure [Terwilliger (1999), Acta Cryst. D55, 1863–1871].
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
The Phd Finger of Human Uhrf1 Reveals a New Subgroup of Unmethylated Histone H3 Tail Readers.
Nada Lallous,Pierre Legrand,Alastair G. McEwen,Santiago Ramón-Maiques,Jean-Pierre Samama,Catherine Birck +5 more
TL;DR: This work shows the binding specificity of the PHD finger of human U HRF1 (huUHRF1-PHD) towards unmodified histone H3 N-terminal tail using native gel electrophoresis and isothermal titration calorimetry and reports the molecular basis of this interaction.
Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography.
TL;DR: The crystal structure of gluconate kinase from Escherichia coli has been determined to 2.0 A resolution by X-ray crystallography and opening of the active site cleft upon ATP binding is the opposite of what has been observed in the NMP kinase family so far.
41
The structure of the TRAPP subunit TPC6 suggests a model for a TRAPP subcomplex.
TL;DR: The 1.7 Å crystal structure of human TPC6, a third TRAPP subunit, strikingly resembles that of BET3, and suggests heterodimerization of TPC 6 and BET3 as shown by in vitro and in vivo association studies.
The Virulence Factor PEB4 (Cj0596) and the Periplasmic Protein Cj1289 Are Two Structurally Related SurA-like Chaperones in the Human Pathogen Campylobacter jejuni
Avinash Kale,Chatchawal Phansopa,Chatrudee Suwannachart,C. Jeremy Craven,John B. Rafferty,David J. Kelly +5 more
TL;DR: The PEB4 protein is an antigenic virulence factor implicated in host cell adhesion, invasion, and colonization in the food-borne pathogen Campylobacter jejuni and two other SurA-like proteins (Cj1289 and Cj0694) are identified, providing the first structural insights into the periplasmic assembly of outer membrane proteins in C. jejuno.
40
Crystal Structure of Activated ModE Reveals Conformational Changes Involving Both Oxyanion and DNA-binding Domains
TL;DR: Manual docking of an idealized DNA structure suggests that this conformational change should improve DNA binding of the activated molybdate-bound ModE.
40
References
Resolution of phase ambiguity in macromolecular crystallography.
TL;DR: The method demonstrates a remarkable effectiveness for overcoming the phase ambiguity problem that has the major obstacle in the use of SIR or SAS data alone for macromolecular studies.
1K
Haloalkane dehalogenases: structure of a Rhodococcus enzyme.
Janet Newman,Thomas S. Peat,Ruth A. Richard,Lynn Kan,Paul E. Swanson,Joseph A. Affholter,Ian Holmes,John F. Schindler,Clifford J. Unkefer,Thomas C. Terwilliger +9 more
TL;DR: The hydrolytic haloalkane dehalogenases are promising bioremediation and biocatalytic agents and it appears that when cocrystallized with NaI the Rhodococcus enzyme has a rare stable S-I covalent bond to S(gamma) of C187.
189
Histogram matching as a new density modification technique for phase refinement and extension of protein molecules
Kam Y. J. Zhang,Peter Main +1 more
TL;DR: In this article, a histogram matching technique was used to refine pig 2Zn insulin phases from a mean error of 60° to one of 46°, with these refined phases as a starting point for phase extension to 1.5 A, the mean error for the final 13 000 phases is 46°.
173
Bias Reduction in Phase Refinement by Modified Interference Functions: Introducing the γ Correction
TL;DR: The scale of the bias component, here denoted as gamma, is shown to be equal in magnitude to the origin vector of the interference function G that defines the relationships between the structure factors.
71