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- PDB-9wls: PSI complex of A.thaliana isolated using DOC based Clear-Native-P... -

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Basic information

Entry
Database: PDB / ID: 9wls
TitlePSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method
Components
  • (Chlorophyll a-b binding protein ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I chlorophyll a/b-binding protein ...) x 2
  • (Photosystem I reaction center subunit ...) x 10
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I complex / membrane protein
Function / homology
Function and homology information


photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / chloroplast membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / chloroplast membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / thylakoid / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / calmodulin binding / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit VIII superfamily / Chlorophyll A-B binding protein / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
: / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...: / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Chem-XAT / Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit VI-2, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsKawamoto, A. / Seki, S. / Kurisu, G.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04958 Japan
Japan Society for the Promotion of Science (JSPS)23H04960 Japan
Citation
Journal: To Be Published
Title: A novel method for cryo-EM protein sample preparation based on Clear-Native-PAGE
Authors: Yang, Z. / Kameo, S. / Seki, S. / Kurisu, G. / Tanaka, R. / Kawamoto, A. / Takabayashi, A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein 6, chloroplastic
2: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
4: Chlorophyll a-b binding protein 4, chloroplastic
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II-2, chloroplastic
E: Photosystem I reaction center subunit IV A, chloroplastic
F: Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit V, chloroplastic
H: Photosystem I reaction center subunit VI-2, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK, chloroplastic
L: Photosystem I reaction center subunit XI, chloroplastic
N: Photosystem I reaction center subunit N, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)586,323223
Polymers443,50217
Non-polymers142,821206
Water8,647480
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Chlorophyll a-b binding protein ... , 2 types, 2 molecules 14

#1: Protein Chlorophyll a-b binding protein 6, chloroplastic / LHCI-730 / LHCII type III CAB-6 / Light-harvesting complex protein Lhca1


Mass: 26021.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q01667
#4: Protein Chlorophyll a-b binding protein 4, chloroplastic / LHCI type III CAB-4


Mass: 27760.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P27521

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Photosystem I chlorophyll a/b-binding protein ... , 2 types, 2 molecules 23

#2: Protein Photosystem I chlorophyll a/b-binding protein 2, chloroplastic / Lhca2 / LHCI type III LHCA2


Mass: 27782.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SYW8
#3: Protein Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Lhca3*1 / LHCI type III LHCA3


Mass: 29206.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#5: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 83315.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56766, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82555.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56767, photosystem I

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Photosystem I reaction center subunit ... , 10 types, 10 molecules DEFGHIJKLN

#8: Protein Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I 20 kDa subunit 2 / PSI-D2


Mass: 22336.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SA56
#9: Protein Photosystem I reaction center subunit IV A, chloroplastic / PSI-E A


Mass: 14984.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S831
#10: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 24203.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SHE8
#11: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G


Mass: 17103.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7N7
#12: Protein Photosystem I reaction center subunit VI-2, chloroplastic / PSI-H1


Mass: 15291.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI6
#13: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 4137.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56768
#14: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 5011.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56769
#15: Protein Photosystem I reaction center subunit psaK, chloroplastic / PSI-K / Photosystem I subunit X


Mass: 13219.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI5
#16: Protein Photosystem I reaction center subunit XI, chloroplastic / PSI-L / PSI subunit V


Mass: 23070.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI4
#17: Protein Photosystem I reaction center subunit N, chloroplastic / PSI-N


Mass: 18451.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49107

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Protein / Sugars , 2 types, 2 molecules C

#29: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#7: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 9049.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62090, photosystem I

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Non-polymers , 12 types, 685 molecules

#18: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 117 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 29 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-A1LXP / Lutein / (3R,3'R,6'R)-beta,epsilon-Carotene-3,3'-diol / (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#30: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method
Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.5 / Details: 25mM Bis-Tris, 0.05% a-DDM
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMBis(2-hydroxyethyl)iminotris(hydroxymethyl)methaneBis-Tris1
20.05 %n-Dodecyl-a-D-maltosideDDM1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.651 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8764
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Spherical aberration corrector: Microscope was modified with Cs corrector

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
4CTFFIND4.1CTF correction
7UCSF ChimeraX1.9model fitting
8Coot0.9.8.7model fitting
10RELION4.0.2initial Euler assignment
11RELION4.0.2final Euler assignment
12RELION4.0.2classification
13RELION4.0.23D reconstruction
20Servalcat0.4.115model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1629453
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148985 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 40.0832 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8J7B

8j7b


Accession code: 8J7B / Source name: PDB / Type: experimental model
RefinementResolution: 2.18→264.6 Å / Num. reflection obs: 3745273 / Average fsc work: 0.8725 / Cross valid method: NONE
Displacement parametersBiso mean: 59.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0196379250.0143
ELECTRON MICROSCOPYs_angle_nonh_deg2.0721538122.0058
ELECTRON MICROSCOPYs_dihedral_angle_1_deg6.531532495
ELECTRON MICROSCOPYs_dihedral_angle_2_deg3.5484720215281.701
ELECTRON MICROSCOPYs_dihedral_angle_3_deg12.0455678410.4857
ELECTRON MICROSCOPYs_dihedral_angle_6_deg15.1713147210
ELECTRON MICROSCOPYs_chiral_restr0.099945070.1388
ELECTRON MICROSCOPYs_planes0.0106708320.0206
ELECTRON MICROSCOPYs_nbd0.2201522930.2
ELECTRON MICROSCOPYs_nbtor0.2373542880.2
ELECTRON MICROSCOPYs_hbond_nbd0.161210250.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.18-2.196ELECTRON MICROSCOPY805630.6236
2.196-2.214ELECTRON MICROSCOPY909010.6513
2.214-2.233ELECTRON MICROSCOPY883890.6715
2.233-2.252ELECTRON MICROSCOPY869470.6866
2.252-2.271ELECTRON MICROSCOPY864930.6988
2.271-2.291ELECTRON MICROSCOPY849250.7185
2.291-2.311ELECTRON MICROSCOPY824970.7373
2.311-2.331ELECTRON MICROSCOPY820510.7525
2.331-2.352ELECTRON MICROSCOPY803290.766
2.352-2.373ELECTRON MICROSCOPY789330.7766
2.373-2.394ELECTRON MICROSCOPY766990.7857
2.395-2.416ELECTRON MICROSCOPY759570.7985
2.416-2.439ELECTRON MICROSCOPY753250.8086
2.439-2.461ELECTRON MICROSCOPY731550.8149
2.461-2.484ELECTRON MICROSCOPY717970.8263
2.485-2.508ELECTRON MICROSCOPY702970.8394
2.508-2.532ELECTRON MICROSCOPY702690.8516
2.532-2.556ELECTRON MICROSCOPY669430.8608
2.557-2.581ELECTRON MICROSCOPY668610.8673
2.581-2.607ELECTRON MICROSCOPY654970.875
2.607-2.633ELECTRON MICROSCOPY640950.8826
2.633-2.659ELECTRON MICROSCOPY629050.8906
2.659-2.686ELECTRON MICROSCOPY610450.8977
2.686-2.714ELECTRON MICROSCOPY611490.9064
2.714-2.742ELECTRON MICROSCOPY593830.9133
2.742-2.771ELECTRON MICROSCOPY579450.9186
2.771-2.8ELECTRON MICROSCOPY561610.9226
2.8-2.83ELECTRON MICROSCOPY553630.9278
2.83-2.86ELECTRON MICROSCOPY542730.933
2.861-2.892ELECTRON MICROSCOPY531730.9388
2.892-2.923ELECTRON MICROSCOPY518850.9419
2.924-2.956ELECTRON MICROSCOPY512950.9446
2.956-2.99ELECTRON MICROSCOPY498450.9496
2.99-3.024ELECTRON MICROSCOPY486370.9542
3.024-3.059ELECTRON MICROSCOPY472390.9562
3.059-3.094ELECTRON MICROSCOPY465690.959
3.095-3.131ELECTRON MICROSCOPY457690.9627
3.131-3.169ELECTRON MICROSCOPY440670.9649
3.169-3.207ELECTRON MICROSCOPY432730.9666
3.207-3.246ELECTRON MICROSCOPY423330.9694
3.247-3.287ELECTRON MICROSCOPY415930.9711
3.287-3.328ELECTRON MICROSCOPY400150.972
3.328-3.37ELECTRON MICROSCOPY391890.9725
3.371-3.414ELECTRON MICROSCOPY378610.9742
3.414-3.459ELECTRON MICROSCOPY374550.9761
3.459-3.504ELECTRON MICROSCOPY363730.9773
3.505-3.551ELECTRON MICROSCOPY350130.9776
3.552-3.6ELECTRON MICROSCOPY348490.9781
3.6-3.649ELECTRON MICROSCOPY333430.9778
3.65-3.7ELECTRON MICROSCOPY328650.9772
3.701-3.753ELECTRON MICROSCOPY312850.9776
3.753-3.807ELECTRON MICROSCOPY306030.9782
3.807-3.862ELECTRON MICROSCOPY303130.9782
3.863-3.92ELECTRON MICROSCOPY287410.9787
3.92-3.978ELECTRON MICROSCOPY284550.9794
3.979-4.039ELECTRON MICROSCOPY271570.9795
4.04-4.102ELECTRON MICROSCOPY270450.9795
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