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- PDB-4ixq: RT fs X-ray diffraction of Photosystem II, dark state -

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Basic information

Entry
Database: PDB / ID: 4ixq
TitleRT fs X-ray diffraction of Photosystem II, dark state
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 16
  • Cytochrome c-550
  • Photosystem Q(B) protein 1
KeywordsPHOTOSYNTHESIS / iron / manganese / PS II / PS2 / transmembrane alpha-helix / electron transport / reaction center / water oxidation / membrane complex / thylakoid membrane
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising ...Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem II protein D1 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 1 / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 5.7 Å
AuthorsKern, J. / Alonso-Mori, R. / Tran, R. / Hattne, J. / Gildea, R.J. / Echols, N. / Gloeckner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. ...Kern, J. / Alonso-Mori, R. / Tran, R. / Hattne, J. / Gildea, R.J. / Echols, N. / Gloeckner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Koroidov, S. / Lampe, A. / Han, G. / Gul, S. / DiFiore, D. / Milathianaki, D. / Fry, A.R. / Miahnahri, A. / Schafer, D.W. / Messerschmidt, M. / Seibert, M.M. / Koglin, J.E. / Sokaras, D. / Weng, T.-C. / Sellberg, J. / Latimer, M.J. / Grosse-Kunstleve, R.W. / Zwart, P.H. / White, W.E. / Glatzel, P. / Adams, P.D. / Bogan, M.J. / Williams, G.J. / Boutet, S. / Messinger, J. / Zouni, A. / Sauter, N.K. / Yachandra, V.K. / Bergmann, U. / Yano, J.
CitationJournal: Science / Year: 2013
Title: Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.
Authors: Kern, J. / Alonso-Mori, R. / Tran, R. / Hattne, J. / Gildea, R.J. / Echols, N. / Glockner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Koroidov, S. / Lampe, A. / ...Authors: Kern, J. / Alonso-Mori, R. / Tran, R. / Hattne, J. / Gildea, R.J. / Echols, N. / Glockner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Koroidov, S. / Lampe, A. / Han, G. / Gul, S. / Difiore, D. / Milathianaki, D. / Fry, A.R. / Miahnahri, A. / Schafer, D.W. / Messerschmidt, M. / Seibert, M.M. / Koglin, J.E. / Sokaras, D. / Weng, T.C. / Sellberg, J. / Latimer, M.J. / Grosse-Kunstleve, R.W. / Zwart, P.H. / White, W.E. / Glatzel, P. / Adams, P.D. / Bogan, M.J. / Williams, G.J. / Boutet, S. / Messinger, J. / Zouni, A. / Sauter, N.K. / Yachandra, V.K. / Bergmann, U. / Yano, J.
History
DepositionJan 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2May 8, 2013Group: Database references
Revision 2.0Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.pdbx_stereo_config / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem Q(B) protein 1
B: Photosystem II core light harvesting protein
C: Photosystem II CP43 protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
y: Photosystem II reaction center protein ycf12
X: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
Y: Photosystem II reaction center protein Y
a: Photosystem Q(B) protein 1
b: Photosystem II core light harvesting protein
c: Photosystem II CP43 protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
g: Photosystem II reaction center protein ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
G: Photosystem II reaction center protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)765,686224
Polymers630,09940
Non-polymers135,587184
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.864, 227.511, 307.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules AaVv

#1: Protein Photosystem Q(B) protein 1 / 32 kDa thylakoid membrane protein 1 / Photosystem II protein D1 1


Mass: 39762.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A444, photosystem II
#16: Protein Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A386

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Photosystem II ... , 16 types, 32 molecules BbCcDdHhIiJjKkLlMmOoTtUuygXxZzYG

#2: Protein Photosystem II core light harvesting protein


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ1
#3: Protein Photosystem II CP43 protein


Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIF8
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8CM25, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L / PSII 5 kDa protein


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7
#13: Protein Photosystem II manganese-stabilizing polypeptide / MSP


Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / PSII-T / PSII-Tc


Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ0
#15: Protein Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein ycf12


Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center X protein


Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1R6
#19: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHJ2
#20: Protein/peptide Photosystem II reaction center protein Y


Mass: 2400.951 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN9

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Sugars , 2 types, 28 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C51H96O15
#33: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 13 types, 156 molecules

#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#22: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#24: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#25: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C53H80O2
#26: Chemical ChemComp-OEC / OXYGEN EVOLVING SYSTEM


Mass: 323.828 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O4
#27: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56
#29: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#30: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H78O12S
#31: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10
#32: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#34: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#35: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF CHAINS Y AND G IS KNOWN BUT WAS MODELED AS POLYALANINE DUE TO POOR DENSITY. THE ...THE SEQUENCE OF CHAINS Y AND G IS KNOWN BUT WAS MODELED AS POLYALANINE DUE TO POOR DENSITY. THE ACTUAL SEQUENCE MATCHES UNIPROT REFERENCE Q8DKM3: MET ASP TRP ARG VAL LEU VAL VAL LEU LEU PRO VAL LEU LEU ALA ALA GLY TRP ALA VAL ARG ASN ILE LEU PRO TYR ALA VAL LYS GLN VAL GLN LYS LEU LEU GLN LYS ALA LYS ALA ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4663

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.36 %
Crystal growTemperature: 298 K / Method: batch / pH: 7
Details: 4% PEG2000, 5 mM calcium chloride, 100 mM PIPES, pH 7.0, BATCH, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.2967, 1.7546
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Dec 4, 2011 / Details: KB mirrors
RadiationMonochromator: No monochromator, FEL beam with 20-30 eV bandwidth
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.29671
21.75461
ReflectionResolution: 5.7→82.94 Å / Num. all: 27691 / Num. obs: 27220 / % possible obs: 98.3 % / Observed criterion σ(I): 3.3 / Redundancy: 54.2 % / Net I/σ(I): 26.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsDiffraction-ID% possible all
5.7-5.933.53.3186
5.93-6.2198
6.2-6.521100
6.52-6.931100
6.93-7.471100
7.47-8.221100
8.22-9.411100
9.41-11.851100
11.85-82.941100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1265)refinement
cctbx.xfeldata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BZ1

3bz1
PDB Unreleased entry


Resolution: 5.7→82.936 Å / SU ML: 0.91 / σ(F): 1.4 / σ(I): 3.2 / Phase error: 30.17 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3142 1325 4.87 %FROM PDB ENTRY 3BZ1, EXPANDED TO INCLUDE 5% OF REFLECTIONS
Rwork0.277 ---
obs0.2788 27201 98.23 %-
all-27691 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.7→82.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41050 0 9182 0 50232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552048
X-RAY DIFFRACTIONf_angle_d1.02771500
X-RAY DIFFRACTIONf_dihedral_angle_d18.50818416
X-RAY DIFFRACTIONf_chiral_restr0.0527286
X-RAY DIFFRACTIONf_plane_restr0.0058770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
5.7-5.92820.34031230.31732442256586
5.9282-6.19790.36151570.3052825298298
6.1979-6.52460.3691400.299728813021100
6.5246-6.93320.33611540.279129073061100
6.9332-7.46820.35821510.265728753026100
7.4682-8.21910.26471520.239729263078100
8.2191-9.4070.27591470.227529473094100
9.407-11.84640.26321550.249129503105100
11.8464-82.94460.31431460.316431233269100

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