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- PDB-9v3d: SFX structure of 3-5 micrometers Lysozyme microcrystals -

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Basic information

Entry
Database: PDB / ID: 9v3d
TitleSFX structure of 3-5 micrometers Lysozyme microcrystals
ComponentsLysozyme C
KeywordsHYDROLASE / Time-resolved XFEL SFX / Lysozyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / defense response to Gram-positive bacterium / endoplasmic reticulum / : / 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
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLuo, F. / Kang, J. / Tono, K. / Iwata, S. / Nango, E.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101070 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121001 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)24H02262 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)24H00547 Japan
CitationJournal: J.Appl.Crystallogr. / Year: 2026
Title: Compact tape-driven sample delivery system for serial femtosecond crystallography.
Authors: Kang, J. / Shimazu, Y. / Luo, F. / Yamashita, A. / Tanaka, T. / Inubushi, Y. / Tono, K. / Nuemket, N. / Orville, A.M. / Iwata, S. / Nango, E. / Yabashi, M.
History
DepositionMay 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4845
Polymers14,3311
Non-polymers1534
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.450, 79.450, 38.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21A-376-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 290 K / Method: batch mode / pH: 3 / Details: 8% PEG 6000, 4.8 M NaCl, and 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Apr 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.68→39.73 Å / Num. obs: 14477 / % possible obs: 100 % / Redundancy: 202.5 % / CC1/2: 0.97 / Net I/σ(I): 7.46
Reflection shellResolution: 1.68→1.7 Å / Redundancy: 23.7 % / Num. unique obs: 697 / CC1/2: 0.6994
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrystFELdata scaling
CrystFELdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→39.73 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 721 4.99 %
Rwork0.1928 --
obs0.1945 14443 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 7 77 1076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071048
X-RAY DIFFRACTIONf_angle_d0.9581423
X-RAY DIFFRACTIONf_dihedral_angle_d5.623153
X-RAY DIFFRACTIONf_chiral_restr0.065148
X-RAY DIFFRACTIONf_plane_restr0.008189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.810.46351400.42685X-RAY DIFFRACTION100
1.81-1.990.23261410.18262680X-RAY DIFFRACTION100
1.99-2.280.2361420.19412717X-RAY DIFFRACTION100
2.28-2.870.22091450.17842745X-RAY DIFFRACTION100
2.87-39.730.20191530.17992895X-RAY DIFFRACTION100

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