XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps

Abstract Protoplanetary disks are dust- and gas-rich structures surrounding protostars. Depending on the distance from the protostar, this dust is thermally processed to different degrees and accreted to form bodies of varying chemical compositions. The primordial accretion processes occurring in the early protoplanetary disk such as chondrule formation and metal segregation are not well understood. One way to constrain them is to study the morphology and composition of forsteritic grains from the matrix of carbonaceous chondrites. Here, we present high-resolution ptychographic X-ray nanotomography and multimodal chemical microtomography (X-ray diffraction and X-ray fluorescence) to reveal the early history of forsteritic grains extracted from the matrix of the Murchison CM2.5 chondrite. The 3D electron density maps revealed, at unprecedented resolution (64 nm), spherical inclusions containing Fe–Ni, very little silica-rich glass and void caps (i.e., volumes where the electron density is consistent with conditions close to vacuum) trapped in forsterite. The presence of the voids along with the overall composition, petrological textures, and shrinkage calculations is consistent with the grains experiencing one or more heating events with peak temperatures close to the melting point of forsterite (∼2100 K), and subsequently cooled and contracted, in agreement with chondrule-forming conditions.

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The accuracy of electron-density maps in X-ray analysis with special reference to dibenzyl

Acta Crystallographica ◽

10.1107/s0365110x49000175 ◽

1949 ◽

Vol 2 (2) ◽

pp. 65-82 ◽

Cited By ~ 215

Author(s):

D. W. J. Cruickshank

Keyword(s):

Special Reference ◽

Electron Density ◽

X Ray ◽

Density Maps

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Electron Density Distribution in LiB3O5 at 293 K

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768197007817 ◽

1997 ◽

Vol 53 (6) ◽

pp. 870-879 ◽

Cited By ~ 19

Author(s):

C. Le Hénaff ◽

N. K. Hansen ◽

J. Protas ◽

G. Marnier

Keyword(s):

Density Distribution ◽

Electron Density ◽

Electron Density Distribution ◽

X Ray Diffraction ◽

X Ray ◽

Hartree Fock ◽

Density Maps ◽

Symmetry Constraints ◽

Net Charges ◽

Good Agreement

The electron density distribution in lithium triborate LiB3O5 has been studied at room temperature by X-ray diffraction using Ag K \alpha radiation up to 1.02 Å−1 [1439 unique reflections with I > 3\sigma(I)]. Conventional refinements with a free-atom model yield R(F) = 0.0223, wR(F) = 0.0299, S = 1.632. Atom charge refinements show that the lithium should be considered a monovalent ion. Multipolar refinements were undertaken up to fourth order, imposing local non-crystallographic symmetry constraints in order to avoid phase problems leading to meaningless multipole populations due to the non-centrosymmetry of the structure (space group: Pn a21). The residual indices decreased to: R(F) = 0.0147, wR(F) = 0.0193, S = 1.106. The net charges are in good agreement with what can be expected in borate chemistry. Deformation density maps are analysed in terms of \sigma and \pi bonding. The experimental electron distribution in the p z orbitals of triangular B atoms and surrounding O atoms has been analysed by introducing idealized hybridized states. In parallel, the electron density has been determined from ab initio Hartree–Fock calculations on fragments of the structure. Agreement with the X-ray determination is very good and confirms the nature of bonding in the crystal. The amount of transfer of \pi electrons from the oxygen to the triangular B atoms is estimated to be 0.22 electrons by theory.

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A chemical interpretation of protein electron density maps in the worldwide protein data bank

10.1101/613109 ◽

2019 ◽

Cited By ~ 3

Author(s):

Sen Yao ◽

Hunter N.B. Moseley

Keyword(s):

Protein Data Bank ◽

Electron Density ◽

Structural Model ◽

Data Bank ◽

X Ray ◽

New Methods ◽

Link Type ◽

Density Maps ◽

Structure Factors ◽

Python Package

AbstractHigh-quality three-dimensional structural data is of great value for the functional interpretation of biomacromolecules, especially proteins; however, structural quality varies greatly across the entries in the worldwide Protein Data Bank (wwPDB). Since 2008, the wwPDB has required the inclusion of structure factors with the deposition of x-ray crystallographic structures to support the independent evaluation of structures with respect to the underlying experimental data used to derive those structures. However, interpreting the discrepancies between the structural model and its underlying electron density data is difficult, since derived electron density maps use arbitrary electron density units which are inconsistent between maps from different wwPDB entries. Therefore, we have developed a method that converts electron density values into units of electrons. With this conversion, we have developed new methods that can evaluate specific regions of an x-ray crystallographic structure with respect to a physicochemical interpretation of its corresponding electron density map. We have systematically compared all deposited x-ray crystallographic protein models in the wwPDB with their underlying electron density maps, if available, and characterized the electron density in terms of expected numbers of electrons based on the structural model. The methods generated coherent evaluation metrics throughout all PDB entries with associated electron density data, which are consistent with visualization software that would normally be used for manual quality assessment. To our knowledge, this is the first attempt to derive units of electrons directly from electron density maps without the aid of the underlying structure factors. These new metrics are biochemically-informative and can be extremely useful for filtering out low-quality structural regions from inclusion into systematic analyses that span large numbers of PDB entries. Furthermore, these new metrics will improve the ability of non-crystallographers to evaluate regions of interest within PDB entries, since only the PDB structure and the associated electron density maps are needed. These new methods are available as a well-documented Python package on GitHub and the Python Package Index under a modified Clear BSD open source license.Author summaryElectron density maps are very useful for validating the x-ray structure models in the Protein Data Bank (PDB). However, it is often daunting for non-crystallographers to use electron density maps, as it requires a lot of prior knowledge. This study provides methods that can infer chemical information solely from the electron density maps available from the PDB to interpret the electron density and electron density discrepancy values in terms of units of electrons. It also provides methods to evaluate regions of interest in terms of the number of missing or excessing electrons, so that a broader audience, such as biologists or bioinformaticians, can also make better use of the electron density information available in the PDB, especially for quality control purposes.Software and full results available athttps://github.com/MoseleyBioinformaticsLab/pdb_eda (software on GitHub)https://pypi.org/project/pdb-eda/ (software on PyPI)https://pdb-eda.readthedocs.io/en/latest/ (documentation on ReadTheDocs)https://doi.org/10.6084/m9.figshare.7994294 (code and results on FigShare)

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Building brain network in electron density map determined by micro-CT

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314082473 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1752-C1752

Author(s):

Rino Saiga ◽

Susumu Takekoshi ◽

Naoya Nakamura ◽

Akihisa Takeuchi ◽

Kentaro Uesugi ◽

...

Keyword(s):

Density Distribution ◽

Electron Density ◽

Electron Density Distribution ◽

Model Building ◽

Three Dimensional ◽

Brain Network ◽

X Ray ◽

Density Maps ◽

Density Map ◽

Electron Density Map

In macromolecular crystallography, an electron density distribution is traced to build a model of the target molecule. We applied this method to model building for electron density maps of a brain network. Human cerebral tissue was stained with heavy atoms [1]. The sample was then analyzed at the BL20XU beamline of SPring-8 to obtain a three-dimensional map of X-ray attenuation coefficients representing the electron density distribution. Skeletonized wire models were built by placing and connecting nodes in the map [2], as shown in the figure below. The model-building procedures were similar to those reported for crystallographic analyses of macromolecular structures, while the neuronal network was automatically traced by using a Sobel filter. Neuronal circuits were then analytically resolved from the skeletonized models. We suggest that X-ray microtomography along with model building in the electron density map has potential as a method for understanding three-dimensional microstructures relevant to biological functions.

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Statistical quality indicators for electron-density maps

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444911035918 ◽

2012 ◽

Vol 68 (4) ◽

pp. 454-467 ◽

Cited By ~ 82

Author(s):

Ian J. Tickle

Keyword(s):

Electron Density ◽

Statistical Significance ◽

Significance Test ◽

Real Space ◽

Structure Model ◽

Space Correlation ◽

The Real ◽

Difference Density ◽

Density Maps ◽

The Difference

The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ2 significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

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Visualization of lipid bilayer in the crystals by solvent contrast modulation

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314085015 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1498-C1498

Author(s):

Yoshiyuki Norimatsu ◽

Junko Tsueda ◽

Ayami Hirata ◽

Shiho Iwasawa ◽

Chikashi Toyoshima

Keyword(s):

Lipid Bilayer ◽

Electron Density ◽

Lipid Bilayers ◽

Transmembrane Helix ◽

Real Space ◽

New Method ◽

Imaging Plate ◽

Salt Bridges ◽

Transmembrane Helices ◽

X Ray

A new method of X-ray solvent contrast modulation was developed to visualize lipid bilayers in crystals of membrane proteins at a high enough resolution to resolve individual phospholipids molecules (~3.5 Å ). Visualization of lipid bilayer has been escaping from conventional crystallographic methods due to its extreme flexibility, and our knowledge on the behavior of lipid bilayer is still very much limited. Here we applied the new method of X-ray solvent contrast modulation to crystals of Ca2+-ATPase in 4 different physiological states. As phospholipids have to be added to make crystals of Ca2+-ATPase, it is expected that lipid bilayers are present in the crystals. Moreover, transmembrane helices of Ca2+-ATPase rearrange drastically during the reaction cycle and some of them show substantial movements perpendicular to the bilayer plane. Thus these crystals provide a rare opportunity to directly visualize phospholipids interacting with a membrane protein in different conformations. Complete diffraction data covering from 200 to 3.2 Å resolution were collected at BL41XU, Spring-8, using an R-Axis V imaging plate detector for crystals soaked in solvent of different electron density. A new concept "solvent exchange probability", which should be 1 in the bulk solvent, 0 inside the protein and an intermediate at interface, was introduced and used as a restraint for real space phase improvement. The electron density maps thus obtained clearly show that: (i) Phospholipid molecules surrounding the protein are fixed apparently by Arg/Lys-phosphate salt bridges or Trp-carbonyl hydrogen bonds and follow the movements of transmembrane helices. Movements of as large as 12 Å are allowed. (ii) If the movement of a transmembrane helix exceeds this limit, associated phospholipids change the partners for fixation or change the orientation of the entire protein molecule.

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Transient electron density maps from femtosecond x-ray powder diffraction

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314098994 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C100-C100

Author(s):

Vincent Juvé ◽

Flavio Zamponi ◽

Marcel Holtz ◽

Michael Woerner ◽

Thomas Elsaesser

Keyword(s):

Charge Transfer ◽

Electron Density ◽

Powder Diffraction ◽

Maximum Entropy Method ◽

Entropy Method ◽

X Rays ◽

X Ray ◽

Density Maps ◽

Structure Factors ◽

Diffraction Angle

Ultrashort hard x-ray pulses are sensitive probes of structural dynamics on the picometer length and femtosecond time scales of electronic and atomic motions. Using short hard x-ray pulses as probe in a pump-probe scheme allow to do femtosecond x-ray diffraction experiments [1], which provide transient electron density maps at a femtosecond timescale with a sub-angstrom spatial resolution. In a typical femtosecond x-ray powder diffraction experiment many Debye-Scherrer rings, up to a maximum diffraction angle 2θmax, are recorded for each time delay between the optical pump and the hard x-ray probe. From the diffraction pattern, the change of the diffracted intensity of each rings are monitored. The interference of diffracted x-rays from the many unexcited cells, with known structure factors coming from steady-state measurement, and diffracted x-rays from the few excited cells allows for the detection of the transients structure factors. Problems could arise if the 3D-Fourier transform is directly used because of the abrupt end of the collected information in the reciprocal space (maximum diffraction angle 2θmax). In order to overcome this problem, the Maximum Entropy Method is apply to the data and the transient electron density maps are derived. We apply the femtosecond x-ray powder diffraction technique and the Maximum Entropy Method to study the induced transient polarization by high optical fields on ionic crystals. Such polarizations are connected to a spatial redistribution of electronic charge, which corresponds to a charge transfer between the two ionic compounds [2]. While the charge transfer originates from the anion to the cation in the LiBH and the NaBH4, the LiH exhibits a peculiar behavior: the charge transfer occurs from the cation to the anion. As result from comparison with calculations in the COHSEX framework, this behavior is due to the strong electronic correlations in the LiH [3].

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