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- PDB-8a9e: Lysozyme, 9-11 fs FEL pulses as determined by XTCAV -

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Basic information

Entry
Database: PDB / ID: 8a9e
TitleLysozyme, 9-11 fs FEL pulses as determined by XTCAV
ComponentsLysozyme
KeywordsHYDROLASE / free electron laser
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-DO3 / GADOLINIUM ATOM / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.665 Å
AuthorsBarends, T. / Nass, K. / Gorel, A. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Microcrystallization methods
Authors: Gorel, A. / Nass, K. / Barends, T. / Schlichting, I.
History
DepositionJun 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4555
Polymers14,3311
Non-polymers1,1234
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.750, 77.750, 38.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698
#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32N4O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4
Details: 10 % NaCl, 0.1 M sodium acetate buffer, pH 4.0, soaked in 100 mM gadoteridol 30 min. before data collection

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.393 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.393 Å / Relative weight: 1
ReflectionResolution: 1.64→22.45 Å / Num. obs: 15159 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 0.923 / CC star: 0.98 / R split: 0.237 / Net I/σ(I): 3.4
Reflection shellResolution: 1.64→1.68 Å / % possible obs: 100 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 736 / CC1/2: 0.411 / CC star: 0.763 / R split: 0.83
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4N5R

4n5r


Resolution: 1.665→22.45 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.624 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2396 1512 10.001 %
Rwork0.2011 13607 -
all0.205 --
obs-15119 99.697 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å20 Å20 Å2
2---0.003 Å20 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.665→22.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 58 52 1102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131072
X-RAY DIFFRACTIONr_bond_other_d0.0010.018949
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6511448
X-RAY DIFFRACTIONr_angle_other_deg1.451.5822198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9385127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.82620.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63915164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.871511
X-RAY DIFFRACTIONr_chiral_restr0.090.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021196
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_nbd_refined0.2230.2251
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.2940
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2537
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.236
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0770.26
X-RAY DIFFRACTIONr_nbd_other0.1910.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.27
X-RAY DIFFRACTIONr_mcbond_it1.3521.756511
X-RAY DIFFRACTIONr_mcbond_other1.2881.752510
X-RAY DIFFRACTIONr_mcangle_it1.8882.631637
X-RAY DIFFRACTIONr_mcangle_other1.892.634638
X-RAY DIFFRACTIONr_scbond_it2.4782.12561
X-RAY DIFFRACTIONr_scbond_other2.4762.12562
X-RAY DIFFRACTIONr_scangle_it3.7233.06811
X-RAY DIFFRACTIONr_scangle_other3.7213.061812
X-RAY DIFFRACTIONr_lrange_it4.6521.7031269
X-RAY DIFFRACTIONr_lrange_other4.62521.6861267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.665-1.7080.3781020.304924X-RAY DIFFRACTION99.9026
1.708-1.7550.2481010.253916X-RAY DIFFRACTION100
1.755-1.8060.2581000.238888X-RAY DIFFRACTION100
1.806-1.8610.252960.229868X-RAY DIFFRACTION100
1.861-1.9210.257930.199833X-RAY DIFFRACTION100
1.921-1.9880.245890.205804X-RAY DIFFRACTION100
1.988-2.0630.264880.209807X-RAY DIFFRACTION100
2.063-2.1460.237850.185763X-RAY DIFFRACTION100
2.146-2.2410.211830.189734X-RAY DIFFRACTION100
2.241-2.3490.194780.191706X-RAY DIFFRACTION100
2.349-2.4750.228730.192655X-RAY DIFFRACTION100
2.475-2.6230.266720.206649X-RAY DIFFRACTION100
2.623-2.8010.267660.193601X-RAY DIFFRACTION100
2.801-3.0220.271630.2553X-RAY DIFFRACTION100
3.022-3.3040.203580.195525X-RAY DIFFRACTION100
3.304-3.6850.217530.189482X-RAY DIFFRACTION100
3.685-4.2370.195490.17432X-RAY DIFFRACTION100
4.237-5.1440.25410.205372X-RAY DIFFRACTION100
5.144-7.0970.251320.194300X-RAY DIFFRACTION100
7.097-22.450.25240.218202X-RAY DIFFRACTION100

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