scholarly journals Cryo-EM single-particle structure refinement and map calculation using Servalcat

2021 ◽  
Vol 77 (10) ◽  
Author(s):  
Keitaro Yamashita ◽  
Colin M. Palmer ◽  
Tom Burnley ◽  
Garib N. Murshudov
Keyword(s):  
Single Particle ◽  
Model Building ◽  
Structure Refinement ◽  
Accurate Determination ◽  
Point Group ◽  
Atomic Model ◽  
Group Symmetry ◽  
Particle Analysis ◽  
Model Refinement ◽  
Symmetry Constraints

In 2020, cryo-EM single-particle analysis achieved true atomic resolution thanks to technological developments in hardware and software. The number of high-resolution reconstructions continues to grow, increasing the importance of the accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted F o − F c difference map, which is derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The F o − F c map helps in the visualization of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in the electron-density maps produced by X-ray crystallography, and some H atoms are even visible at ∼1.8 Å resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If point-group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with the appropriate symmetry constraints.

scholarly journals In situ structure determination using single particle cryo-electron microscopy images

2020 ◽  
Author(s):  
Jing Cheng ◽  
Bufan Li ◽  
Long Si ◽  
Xinzheng Zhang
Keyword(s):  
Electron Microscopy ◽  
Structure Determination ◽  
Single Particle ◽  
Structure Refinement ◽  
Target Function ◽  
Target Protein ◽  
Particle Analysis ◽  
Cryo Electron Microscopy ◽  
Tilt Series

AbstractCryo-electron microscopy (cryo-EM) tomography is a powerful tool for in situ structure determination. However, this method requires the acquisition of tilt series, and its time consuming throughput of acquiring tilt series severely slows determination of in situ structures. By treating the electron densities of non-target protein as non-Gaussian distributed noise, we developed a new target function that greatly improves the efficiency of the recognition of the target protein in a single cryo-EM image without acquiring tilt series. Moreover, we developed a sorting function that effectively eliminates the false positive detection, which not only improves the resolution during the subsequent structure refinement procedure but also allows using homolog proteins as models to recognize the target protein. Together, we developed an in situ single particle analysis (isSPA) method. Our isSPA method was successfully applied to solve structures of glycoproteins on the surface of a non-icosahedral virus and Rubisco inside the carboxysome. The cryo-EM data from both samples were collected within 24 hours, thus allowing fast and simple structural determination in situ.

scholarly journals Point-group symmetry detection in three-dimensional charge density of biomolecules

2019 ◽  
Vol 36 (7) ◽  
pp. 2237-2243
Author(s):  
Cyril F Reboul ◽  
Simon Kiesewetter ◽  
Dominika Elmlund ◽  
Hans Elmlund
Keyword(s):  
Charge Density ◽  
Single Particle ◽  
Statistical Tests ◽  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Point Group Symmetry ◽  
Density Maps ◽  
Point Groups ◽  
Density Map

Abstract Motivation No rigorous statistical tests for detecting point-group symmetry in three-dimensional (3D) charge density maps obtained by electron microscopy (EM) and related techniques have been developed. Results We propose a method for determining the point-group symmetry of 3D charge density maps obtained by EM and related techniques. Our ab initio algorithm does not depend on atomic coordinates but utilizes the density map directly. We validate the approach for a range of publicly available single-particle cryo-EM datasets. In straightforward cases, our method enables fully automated single-particle 3D reconstruction without having to input an arbitrarily selected point-group symmetry. When pseudo-symmetry is present, our method provides statistics quantifying the degree to which the 3D density agrees with the different point-groups tested. Availability and implementation The software is freely available at https://github.com/hael/SIMPLE3.0.

scholarly journals Crystal structure of post-perovskite-type CaIrO3reinvestigated: new insights into atomic thermal vibration behaviors

2015 ◽  
Vol 71 (9) ◽  
pp. 1109-1113
Author(s):  
Akihiko Nakatsuka ◽  
Kazumasa Sugiyama ◽  
Akira Yoneda ◽  
Keiko Fujiwara ◽  
Akira Yoshiasa
Keyword(s):  
Crystal Structure ◽  
Atmospheric Pressure ◽  
Structure Refinement ◽  
Point Group ◽  
Group Symmetry ◽  
Point Group Symmetry ◽  
X Ray ◽  
Thermal Vibrations ◽  
Perovskite Type ◽  
Shared Edge

Single crystals of the title compound, the post-perovskite-type CaIrO3[calcium iridium(IV) trioxide], have been grown from a CaCl2flux at atmospheric pressure. The crystal structure consists of an alternate stacking of IrO6octahedral layers and CaO8hendecahedral layers along [010]. Chains formed by edge-sharing of IrO6octahedra (point-group symmetry 2/m..) run along [100] and are interconnected along [001] by sharing apical O atoms to build up the IrO6octahedral layers. Chains formed by face-sharing of CaO8hendecahedra (point-group symmetrym2m) run along [100] and are interconnected along [001] by edge-sharing to build up the CaO8hendecahedral layers. The IrO6octahedral layers and CaO8hendecahedral layers are interconnected by sharing edges. The present structure refinement using a high-power X-ray source confirms the atomic positions determined by Hiraiet al.(2009) [Z. Kristallogr.224, 345–350], who had revised our previous report [Sugaharaet al.(2008).Am. Mineral.93, 1148–1152]. However, the displacement ellipsoids of the Ir and Ca atoms based on the present refinement can be approximated as uniaxial ellipsoids elongating along [100], unlike those reported by Hiraiet al.(2009). This suggests that the thermal vibrations of the Ir and Ca atoms are mutually suppressed towards the Ir...Ca direction across the shared edge because of the dominant repulsion between the two atoms.

scholarly journals In situ structure determination using single particle cryo-electron microscopy images

2020 ◽  
Author(s):  
Jing Cheng ◽  
Bufan Li ◽  
Long Si ◽  
Xinzheng Zhang
Keyword(s):  
Electron Microscopy ◽  
Structure Determination ◽  
Single Particle ◽  
Structure Refinement ◽  
Target Function ◽  
Target Protein ◽  
Particle Analysis ◽  
Cryo Electron Microscopy ◽  
Tilt Series

Abstract Cryo-electron microscopy (cryo-EM) tomography is a powerful tool for in situ structure determination. However, this method requires the acquisition of tilt series, and its time consuming throughput of acquiring tilt series severely slows determination of in situ structures. By treating the electron densities of non-target protein as non-Gaussian distributed noise, we developed a new target function that greatly improves the efficiency of the recognition of the target protein in a single cryo-EM image without acquiring tilt series. Moreover, we developed a sorting function that effectively eliminates the false positive detection, which not only improves the resolution during the subsequent structure refinement procedure but also allows using homolog proteins as models to recognize the target protein. Together, we developed an in situ single particle analysis (isSPA) method. Our isSPA method was successfully applied to solve structures of glycoproteins on the surface of a non-icosahedral virus and Rubisco inside the carboxysome. The cryo-EM data from both samples were collected within 24 hours, thus allowing fast and simple structural determination in situ.

scholarly journals How good are my data and what is the resolution?

2013 ◽  
Vol 69 (7) ◽  
pp. 1204-1214 ◽  
Author(s):  
Philip R. Evans ◽  
Garib N. Murshudov
Keyword(s):  
Model Building ◽  
Point Group ◽  
Simulated Data ◽  
Group Symmetry ◽  
Data Set ◽  
High Resolution Data ◽  
Common Scale ◽  
Scaling Models ◽  
Automated Model Building

Following integration of the observed diffraction spots, the process of `data reduction' initially aims to determine the point-group symmetry of the data and the likely space group. This can be performed with the programPOINTLESS. The scaling program then puts all the measurements on a common scale, averages measurements of symmetry-related reflections (using the symmetry determined previously) and produces many statistics that provide the first important measures of data quality. A new scaling program,AIMLESS, implements scaling models similar to those inSCALAbut adds some additional analyses. From the analyses, a number of decisions can be made about the quality of the data and whether some measurements should be discarded. The effective `resolution' of a data set is a difficult and possibly contentious question (particularly with referees of papers) and this is discussed in the light of tests comparing the data-processing statistics with trials of refinement against observed and simulated data, and automated model-building and comparison of maps calculated with different resolution limits. These trials show that adding weak high-resolution data beyond the commonly used limits may make some improvement and does no harm.

Redetermination of Bis(η4-1,3-cyclohexadiene)monocarbonyliron

2002 ◽  
Vol 57 (5) ◽  
pp. 479-482 ◽  
Author(s):  
Guido J. Reiß
Keyword(s):  
Crystal Structure ◽  
Structure Refinement ◽  
Point Group ◽  
Group Symmetry ◽  
Ambient Conditions ◽  
Normal Range ◽  
Orthorhombic Space Group ◽  
Torsion Angles ◽  
X Ray ◽  
Atomic Coordinates

The crystal structure of bis(η4-1,3-cyclohexadiene)monocarbonyliron has been redetermined by X-ray data. The compound crystallizes in the enantiomorphic, orthorhombic space group P212121 with one complete molecule in the asymmetric unit. For concordance to the originally reported structure, which was determined under ambient conditions, the redetermination has been carried out at room temperature and at low temperature (T = 293 K: a = 7.618(2), b = 8.522(2), c = 17.138(4) Å, V = 1112.6(5) Å3, R1 = 0.0226, wR2 = 0.0539; T = 120 K: a = 7.509(2), b = 8.417(3), c = 16.778(6) Å, V = 1060.3(6) Å3, R1 = 0.0242, wR2 = 0.0533). The redetermination proved this complex to have non-crystallographic C2v point group symmetry. Correlation effects to the atomic coordinates and displacement parameters introduced problems during the structure refinement caused by pseudo-symmetry of the molecule. All bond lengths, angles, and torsion angles appear in this revised crystal structure in the normal range for π-coordinated diene transition metal complexes.

Hydrothermal Synthesis and Solid-State Laser Refrigeration of Ytterbium-Doped Potassium Lutetium Fluoride (KLF) Microcrystals

2020 ◽  
Author(s):  
Xiaojing Xia ◽  
Anupum Pant ◽  
Xuezhe Zhou ◽  
Elena Dobretsova ◽  
Alex Bard ◽  
...  
Keyword(s):  
Hydrothermal Synthesis ◽  
Solid State ◽  
Information Science ◽  
Point Group ◽  
Solid State Laser ◽  
Lanthanide Ions ◽  
Group Symmetry ◽  
Luminescence Spectra ◽  
Crystalline Phases ◽  
State Laser

Fluoride crystals, due to their low phonon energies, are attractive hosts of trivalent lanthanide ions for applications in upconverting phosphors, quantum information science, and solid-state laser refrigeration. In this article, we report the rapid, low-cost hydrothermal synthesis of potassium lutetium fluoride (KLF) microcrystals for applications in solid-state laser refrigeration. Four crystalline phases were synthesized, namely orthorhombic K<sub>2</sub>LuF<sub>5</sub> (Pnma), trigonal KLuF<sub>4</sub> (P3<sub>1</sub>21), orthorhombic KLu<sub>2</sub>F<sub>7</sub> (Pna2<sub>1</sub>), and cubic KLu<sub>3</sub>F<sub>10</sub> (Fm3m), with each phase exhibiting unique microcrystalline morphologies. Luminescence spectra and emission lifetimes of the four crystalline phases were characterized based on the point-group symmetry of trivalent cations. Laser refrigeration was measured by observing both the optomechanical eigenfrequencies of microcrystals on cantilevers in vacuum, and also the Brownian dynamics of optically trapped microcrystals in water. Among all four crystalline phases, the most significant cooling was observed for 10%Yb:KLuF<sub>4</sub> with cooling of 8.6 $\pm$ 2.1 K below room temperature. Reduced heating was observed with 10%Yb:K<sub>2</sub>LuF<sub>5</sub>

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