scholarly journals PyMDA: microcrystal data assembly using Python

2020 ◽  
Vol 53 (1) ◽  
pp. 277-281
Author(s):  
Lina Takemaru ◽  
Gongrui Guo ◽  
Ping Zhu ◽  
Wayne A. Hendrickson ◽  
Sean McSweeney ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Data Quality ◽  
Diffraction Data ◽  
Incomplete Data ◽  
Unit Cell ◽  
Data Sets ◽  
X Ray ◽  
Assembly Method ◽  
Multi Stage ◽  
Recent Developments

The recent developments at microdiffraction X-ray beamlines are making microcrystals of macromolecules appealing subjects for routine structural analysis. Microcrystal diffraction data collected at synchrotron microdiffraction beamlines may be radiation damaged with incomplete data per microcrystal and with unit-cell variations. A multi-stage data assembly method has previously been designed for microcrystal synchrotron crystallography. Here the strategy has been implemented as a Python program for microcrystal data assembly (PyMDA). PyMDA optimizes microcrystal data quality including weak anomalous signals through iterative crystal and frame rejections. Beyond microcrystals, PyMDA may be applicable for assembling data sets from larger crystals for improved data quality.

Crystallization and preliminary X-ray studies of sialidase L from the leech Macrobdella decora

1998 ◽  
Vol 54 (1) ◽  
pp. 111-113 ◽  
Author(s):  
Yu Luo ◽  
Min-yuan Chou ◽  
Su-chen Li ◽  
Yu-teh Li ◽  
Ming Luo
Keyword(s):  
Escherichia Coli ◽  
Unit Cell ◽  
Data Sets ◽  
Molecular Replacement ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
X Ray ◽  
Cell Parameters ◽  
Mercury Derivative ◽  
Macrobdella Decora

Functional monomeric 83 kDa sialidase L, a NeuAcα2→3Gal-specific sialidase from Macrobdella leech, was expressed in Escherichia coli and readily crystallized by a macroseeding technique. The crystal belongs to space group P1 with unit-cell parameters a = 46.4, b = 69.3, c = 72.5 Å, α = 113.5, β = 95.4 and γ = 107.3°. There is one molecule per unit cell, giving a Vm = 2.4 Å3 Da−1 and a solvent content of 40%. Native and mercury-derivative data sets were collected to 2.0 Å resolution. Threading and molecular-replacement calculations confirmed the existence of a bacterial sialidase-like domain.

A batch-wise non-linear fitting and analysis tool for treating large X-ray diffraction data sets

2006 ◽  
Vol 39 (2) ◽  
pp. 262-266 ◽  
Author(s):  
R. J. Davies
Keyword(s):  
Diffraction Data ◽  
Operation Mode ◽  
Large Data ◽  
Scattering Data ◽  
Data Sets ◽  
Analysis Tool ◽  
Data Set ◽  
X Ray ◽  
Linear Fitting ◽  
Non Linear

Synchrotron sources offer high-brilliance X-ray beams which are ideal for spatially and time-resolved studies. Large amounts of wide- and small-angle X-ray scattering data can now be generated rapidly, for example, during routine scanning experiments. Consequently, the analysis of the large data sets produced has become a complex and pressing issue. Even relatively simple analyses become difficult when a single data set can contain many thousands of individual diffraction patterns. This article reports on a new software application for the automated analysis of scattering intensity profiles. It is capable of batch-processing thousands of individual data files without user intervention. Diffraction data can be fitted using a combination of background functions and non-linear peak functions. To compliment the batch-wise operation mode, the software includes several specialist algorithms to ensure that the results obtained are reliable. These include peak-tracking, artefact removal, function elimination and spread-estimate fitting. Furthermore, as well as non-linear fitting, the software can calculate integrated intensities and selected orientation parameters.

X-ray powder diffraction data for tetrazene nitrate monohydrate, C2H9N11O4

2021 ◽  
pp. 1-3
Author(s):  
J. Maixner ◽  
J. Ryšavý
Keyword(s):  
Cell Volume ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

X-ray powder diffraction data, unit-cell parameters, and space group for tetrazene nitrate monohydrate, C2H9N11O4, are reported [a = 5.205(1) Å, b = 13.932(3) Å, c = 14.196(4) Å, β = 97.826(3)°, unit-cell volume V = 1019.8(4) Å3, Z = 4, and space group P21/c]. All measured lines were indexed and are consistent with the P21/c space group. No detectable impurities were observed.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

Crystal data and X-ray powder diffraction data of 2,4-diiodo-4-nitrophenol (disophenol), C6H3I2NO3. More precise X-ray powder diffraction data of p-nitrophenol, C6H5NO3

1996 ◽  
Vol 11 (4) ◽  
pp. 301-304
Author(s):  
Héctor Novoa de Armas ◽  
Rolando González Hernández ◽  
José Antonio Henao Martínez ◽  
Ramón Poméz Hernández
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell ◽  
Crystal Data ◽  
Powder Diffraction Data ◽  
Space Group ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Monoclinic Cell

p-nitrophenol, C6H5NO3, and disophenol, C6H3I2NO3, have been investigated by means of X-ray powder diffraction. The unit cell dimensions were determined from diffractometer methods, using monochromatic CuKα1 radiation, and evaluated by indexing programs. The monoclinic cell found for p-nitrophenol was a=6.159(2) Å, b=8.890(2) Å, c=11.770(2) Å, β=103.04(2)°, Z=4, space group P21 or P2l/m, Dx=1.469 Mg/m3. The monoclinic cell found for disophenol has the dimensions a=8.886(1) Å, b=14.088(2) Å, c=8.521(1) Å, β=91.11(1)°, Z=4, space group P2, P2, Pm or P2/m, Dx=2.438 Mg/m3.

X-ray powder diffraction study of ZnGa2Te4

2002 ◽  
Vol 17 (1) ◽  
pp. 41-43 ◽  
Author(s):  
Rashmi ◽  
U. Dhawan
Keyword(s):  
Diffraction Study ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Tetrahedral Structure ◽  
X Ray ◽  
Cell Parameters ◽  
Ray Density

ZnGa2Te4 was found to crystallize in a defect tetrahedral structure with possible space group I4(82) with Z=2. Complete X-ray powder diffraction data were obtained and the unit cell parameters a and c and X-ray density were calculated. These were a=0.5930(1) nm, c=1.1859(3) nm, and Dx=5.7×103 kg/m3.

X-ray powder diffraction data for ertapenem side chain, C20H19N3O7S

2017 ◽  
Vol 32 (3) ◽  
pp. 203-205
Author(s):  
Xiang Lin ◽  
Wei Ling Zhuo ◽  
Qiao Hong Du ◽  
Xi Lin Peng ◽  
Hui Li
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
Side Chain ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

X-ray powder diffraction data, unit-cell parameters, and space group for ertapenem side chain, C20H19N3O7S, are reported [a = 4.907(6) Å, b = 18.686(3) Å, c = 22.071(1) Å, α = γ = 90°, β = 90.759(5)°, unit-cell volume V = 2023.82 Å3, Z = 4, ρcal = 1.462 g cm−3, and space group P21/c]. All measured lines were indexed and are consistent with the P21/c space group. No detectable impurity was observed.

X-ray powder diffraction data for copper(II), bis[(2E)-3-methoxy-2-[(2,6-dimethylphenyl)imino]-4-[(2,6-dimethylphenyl)imino-κN]-3-pentanolato-κO] complex

2013 ◽  
Vol 28 (4) ◽  
pp. 296-298
Author(s):  
R. Pažout ◽  
J. Maixner ◽  
A.S. Jones ◽  
J. Merna
Keyword(s):  
Cell Volume ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

X-ray powder diffraction data, unit-cell parameters, and space group for a new bis(β-diiminato) Cu(II) complex, C44H54CuN4O4, are reported [a = 8.683(3) Å, b = 11.216(3) Å, c = 11.753(4) Å, α = 66.27(3), β = 84.61(3), γ = 78.85(3), unit-cell volume V = 1027.77 Å3, Z = 1, and space group P-1]. All measured lines were indexed and are consistent with the P-1 space group. No detectable impurity was observed.

X-ray powder diffraction data for deoxyschisandrin

2013 ◽  
Vol 28 (3) ◽  
pp. 231-233 ◽  
Author(s):  
Li Li Zhang ◽  
Qing Qing Pan ◽  
Dan Xiao ◽  
Xiao Qing Wu ◽  
Qing Wang ◽  
...  
Keyword(s):  
Cell Volume ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

X-ray powder diffraction data, unit-cell parameters, and space group for deoxyschisandrin, C24H32O6, are reported [a = 13.083(3) Å, b = 19.563(9) Å, c = 8.805(6) Å, β = 90.472(0)°, unit-cell volume V = 2253.82 Å3, Z = 4, and space group P21]. All measured lines were indexed and are consistent with the P21 space group. No detectable impurity was observed.

X-ray powder diffraction data for lanthanum trilactate trihydrate

2015 ◽  
Vol 30 (2) ◽  
pp. 182-184 ◽  
Author(s):  
R. Pažout ◽  
J. Maixner ◽  
V. Bartůněk
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Organometallic Compound ◽  
Unit Cell Volume ◽  
Unit Cell ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

X-ray powder diffraction data, unit cell parameters, and space group for a new organometallic compound, lanthanum trilactate trihydrate, LaC9H21O12, are reported [a = 9.986(1) Å, b = 9.158(1) Å, c = 11.200(1) Å, α = 115.08(1), β = 117.41(1), γ = 88.61(1), unit cell volume V = 804.70 Å3, Z = 2 and space group P1]. All measured lines were indexed. No detectable impurity was observed.

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