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- PDB-5o2i: An efficient setup for fixed-target, time-resolved serial crystal... -

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Basic information

Entry
Database: PDB / ID: 5o2i
TitleAn efficient setup for fixed-target, time-resolved serial crystallography with optical excitation
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / time-resolved crystallography / serial synchrotron crystallography (SSX)
Function / homology
Function and homology information


haloacetate dehalogenase / haloacetate dehalogenase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchulz, E.C. / Mueller-Werkmeister, H. / Mehrabi, P. / Pai, E.F. / Miller, R.J.D.
CitationJournal: To Be Published
Title: An efficient setup for fixed-target, time-resolved serial crystallography with optical excitation
Authors: Schulz, E.C. / Mueller-Werkmeister, H. / Mehrabi, P. / Pai, E.F. / Miller, R.J.D.
History
DepositionMay 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase


Theoretical massNumber of molelcules
Total (without water)68,1472
Polymers68,1472
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-18 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.423, 80.704, 85.760
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 34073.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 41.42 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 18-20 % (w/v) PEG3350, 200 mM CaCl2, 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2→83.62 Å / Num. obs: 35399 / % possible obs: 99.55 % / Redundancy: 77.15 % / Net I/σ(I): 1.39
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R3U

3r3u


Resolution: 2→83.595 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1998 5.3 %
Rwork0.2096 --
obs0.2113 37681 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→83.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 0 235 4939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034918
X-RAY DIFFRACTIONf_angle_d0.6116708
X-RAY DIFFRACTIONf_dihedral_angle_d15.7783964
X-RAY DIFFRACTIONf_chiral_restr0.042683
X-RAY DIFFRACTIONf_plane_restr0.005883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05010.44791170.44572119X-RAY DIFFRACTION82
2.0501-2.10550.31791460.32022576X-RAY DIFFRACTION100
2.1055-2.16750.32691410.28442549X-RAY DIFFRACTION100
2.1675-2.23740.32321470.25722586X-RAY DIFFRACTION100
2.2374-2.31740.24251410.23832563X-RAY DIFFRACTION100
2.3174-2.41020.28651500.23272563X-RAY DIFFRACTION100
2.4102-2.51990.25931430.2292594X-RAY DIFFRACTION100
2.5199-2.65270.251370.21812575X-RAY DIFFRACTION100
2.6527-2.8190.26151450.21752568X-RAY DIFFRACTION100
2.819-3.03660.23841480.20472601X-RAY DIFFRACTION100
3.0366-3.34220.21351390.19232552X-RAY DIFFRACTION100
3.3422-3.82580.20961490.16222606X-RAY DIFFRACTION100
3.8258-4.82010.16271470.14222590X-RAY DIFFRACTION100
4.8201-83.66810.20911480.16672641X-RAY DIFFRACTION100

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