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- PDB-4fe1: Improving the Accuracy of Macromolecular Structure Refinement at ... -

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Basic information

Entry
Database: PDB / ID: 4fe1
TitleImproving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution
Components(Photosystem I ...) x 12
KeywordsPHOTOSYNTHESIS / photosystem / membrane protein / chlorophyll / chromophore / electron transport / metal-binding / photosystem I / thylakoid / transmembrane / electron transfer / membrane / thylakoidmembrane
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / 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 dicluster domain / 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 A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 ...BETA-CAROTENE / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.9228 Å
AuthorsFromme, R. / Adams, P.D. / Fromme, P. / Levitt, M. / Schroeder, G.F. / Brunger, A.T.
Citation
Journal: Structure / Year: 2012
Title: Improving the accuracy of macromolecular structure refinement at 7 A resolution.
Authors: Brunger, A.T. / Adams, P.D. / Fromme, P. / Fromme, R. / Levitt, M. / Schroder, G.F.
#1: Journal: Nature / Year: 2011
Title: Femtosecond X-ray protein nanocrystallography.
Authors: Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / DePonte, D.P. / Weierstall, U. / Doak, R.B. / Maia, F.R. / Martin, A.V. / ...Authors: Chapman, H.N. / Fromme, P. / Barty, A. / White, T.A. / Kirian, R.A. / Aquila, A. / Hunter, M.S. / Schulz, J. / DePonte, D.P. / Weierstall, U. / Doak, R.B. / Maia, F.R. / Martin, A.V. / Schlichting, I. / Lomb, L. / Coppola, N. / Shoeman, R.L. / Epp, S.W. / Hartmann, R. / Rolles, D. / Rudenko, A. / Foucar, L. / Kimmel, N. / Weidenspointner, G. / Holl, P. / Liang, M. / Barthelmess, M. / Caleman, C. / Boutet, S. / Bogan, M.J. / Krzywinski, J. / Bostedt, C. / Bajt, S. / Gumprecht, L. / Rudek, B. / Erk, B. / Schmidt, C. / Homke, A. / Reich, C. / Pietschner, D. / Struder, L. / Hauser, G. / Gorke, H. / Ullrich, J. / Herrmann, S. / Schaller, G. / Schopper, F. / Soltau, H. / Kuhnel, K.U. / Messerschmidt, M. / Bozek, J.D. / Hau-Riege, S.P. / Frank, M. / Hampton, C.Y. / Sierra, R.G. / Starodub, D. / Williams, G.J. / Hajdu, J. / Timneanu, N. / Seibert, M.M. / Andreasson, J. / Rocker, A. / Jonsson, O. / Svenda, M. / Stern, S. / Nass, K. / Andritschke, R. / Schroter, C.D. / Krasniqi, F. / Bott, M. / Schmidt, K.E. / Wang, X. / Grotjohann, I. / Holton, J.M. / Barends, T.R. / Neutze, R. / Marchesini, S. / Fromme, R. / Schorb, S. / Rupp, D. / Adolph, M. / Gorkhover, T. / Andersson, I. / Hirsemann, H. / Potdevin, G. / Graafsma, H. / Nilsson, B. / Spence, J.C.
#2: Journal: Nature / Year: 2001
Title: Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution.
Authors: Jordan, P. / Fromme, P. / Witt, H.T. / Klukas, O. / Saenger, W. / Krauss, N.
#3: Journal: Nature / Year: 2010
Title: Super-resolution biomolecular crystallography with low-resolution data.
Authors: Schroder, G.F. / Levitt, M. / Brunger, A.T.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references / Derived calculations
Revision 2.0Sep 13, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,700140
Polymers257,16212
Non-polymers102,539128
Water0
1
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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules

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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules

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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,079,100420
Polymers771,48536
Non-polymers307,616384
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules

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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules

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
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,053,648417
Polymers746,03333
Non-polymers307,616384
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area107660 Å2
ΔGint-677 kcal/mol
Surface area286310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)281.000, 281.000, 165.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Photosystem I ... , 12 types, 12 molecules ABCDEFIJKLMX

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83267.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A405, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 82992.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A407, photosystem I
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8678.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A415, photosystem I
#4: Protein Photosystem I reaction center subunit II / / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15258.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A420
#5: Protein Photosystem I reaction center subunit IV / / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8268.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A423
#6: Protein Photosystem I reaction center subunit III / / PSI-F


Mass: 17716.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A401
#7: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 4297.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A427
#8: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4770.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A429
#9: Protein Photosystem I reaction center subunit PsaK / / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A425
#10: Protein Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 16156.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DGB4
#11: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3426.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A403
#12: Protein/peptide Photosystem I 4.8K protein /


Mass: 3845.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DKP6

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Non-polymers , 7 types, 128 molecules

#13: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#15: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#16: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#17: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#18: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#19: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 7.32 Å3/Da / Density % sol: 83.2 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.4
Details: beta-dodecylmaltoside, magnesium sulfate, pH 6.4, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2010
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.9→247.463 Å / Num. all: 33699 / Num. obs: 33699 / % possible obs: 97.59 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1058)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JB0

1jb0


Resolution: 4.9228→97.971 Å / SU ML: 0.83 / σ(F): 0 / Phase error: 31.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3145 1528 4.69 %Random
Rwork0.2744 ---
all0.2762 32597 --
obs0.2762 32597 96.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.9228→97.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17394 0 6603 0 23997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125423
X-RAY DIFFRACTIONf_angle_d1.69536034
X-RAY DIFFRACTIONf_dihedral_angle_d21.84110304
X-RAY DIFFRACTIONf_chiral_restr0.0982860
X-RAY DIFFRACTIONf_plane_restr0.0083882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.9228-5.08170.3462540.29982126X-RAY DIFFRACTION71
5.0817-5.26330.32961440.28612681X-RAY DIFFRACTION93
5.2633-5.4740.31731320.27742868X-RAY DIFFRACTION98
5.474-5.72310.32071420.27472906X-RAY DIFFRACTION99
5.7231-6.02480.33881540.27252868X-RAY DIFFRACTION100
6.0248-6.40220.33481470.27782934X-RAY DIFFRACTION100
6.4022-6.89640.31521390.27682913X-RAY DIFFRACTION100
6.8964-7.59020.30741460.26232931X-RAY DIFFRACTION100
7.5902-8.68790.29121750.25162893X-RAY DIFFRACTION100
8.6879-10.94350.30291610.24572936X-RAY DIFFRACTION100
10.9435-97.98990.29781340.29913013X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67720.07280.50850.06280.21961.1284-0.29060.1690.8546-0.0079-0.20330.4453-0.83960.2237-0.56070.52150.26960.12350.9844-0.04720.9147115.1546139.712877.8696
20.2891-0.2966-0.04730.51460.09110.0514-0.20210.33980.6579-0.3299-0.00720.313-0.4033-0.2254-0.5769-0.08221.03190.41390.7137-0.15560.41483.773497.865278.6361
30.00410.0060.00110.006-0.00470.0093-0.0153-0.0573-0.02290.11230.122-0.0495-0.0767-0.02370.02880.25440.45620.02171.04240.16940.5346100.9589114.830338.2087
40.0404-0.05-0.01550.09260.01480.00650.0158-0.0010.0546-0.033-0.0473-0.0679-0.0184-0.05390.08280.55950.53960.19840.66330.11380.4979115.5108115.626237.0618
50.0445-0.01350.05030.1093-0.07830.08810.03140.0372-0.0986-0.0135-0.1211-0.00970.07050.0154-0.02630.49160.4811-0.06851.44110.34161.037980.9737125.87536.8147
60.0615-0.0498-0.0604-0.0189-0.0243-0.00030.06420.01610.0022-0.1365-0.0513-0.0002-0.05040.04250.01190.26510.51240.18140.6592-0.11231.081668.8548135.305977.7809
70.0239-0.0157-0.00480.0681-0.01760.029-0.024-0.06310.06470.0677-0.00950.0326-0.04630.0167-0.0640.09180.0937-0.04720.2505-0.10850.0476114.897587.192378.7342
80.01040.01160.00840.00980.01210.0116-0.1894-0.0154-0.02560.21-0.0830.2030.0338-0.0904-0.00010.64510.2644-0.0640.9209-0.26551.097277.4517147.364879.6294
90.0074-0.00520.0023-0.0041-0.00140.00020.0449-0.1707-0.044-0.01020.02190.0092-0.05990.0236-00.4627-0.12760.22350.87890.15670.8256147.5707160.099674.6319
100.25270.2003-0.15380.2485-0.02920.29550.2946-0.2290.0034-0.04410.0045-0.4783-0.07070.21640.10310.16210.0443-0.01920.3368-0.00080.2946137.640296.04872.1222
110.27020.0979-0.04960.0892-0.10480.1575-0.14750.3232-0.0783-0.05630.0099-0.0060.0757-0.0314-0.05450.26210.17830.15720.5489-0.11770.462102.144473.199776.9087
120.0111-0.01560.00270.00150.0007-0.00010.125-0.0023-0.01290.0159-0.03240.0164-0.0242-0.0381-0.00020.65140.24970.05720.59610.04080.969554.7325113.153875.647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:755 OR RESID 801:854 OR RESID 856 ) ) OR ( CHAIN J AND RESID 1101:1101 )A13 - 755
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:755 OR RESID 801:854 OR RESID 856) ) OR ( CHAIN J AND RESID 1101:1101 )A801 - 856
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 13:755 OR RESID 801:854 OR RESID 856) ) OR ( CHAIN J AND RESID 1101:1101 )J1101
4X-RAY DIFFRACTION2( CHAIN I AND RESID 101:101 ) OR ( CHAIN X AND RESID 101:101 ) OR ( CHAIN B AND ( RESID 1:739 OR RESID 801:848 ) ) OR ( CHAIN M AND RESID 1201:1201 )I101
5X-RAY DIFFRACTION2( CHAIN I AND RESID 101:101 ) OR ( CHAIN X AND RESID 101:101 ) OR ( CHAIN B AND ( RESID 1:739 OR RESID 801:848 ) ) OR ( CHAIN M AND RESID 1201:1201 )X101
6X-RAY DIFFRACTION2( CHAIN I AND RESID 101:101 ) OR ( CHAIN X AND RESID 101:101 ) OR ( CHAIN B AND ( RESID 1:739 OR RESID 801:848 ) ) OR ( CHAIN M AND RESID 1201:1201 )B1 - 739
7X-RAY DIFFRACTION2( CHAIN I AND RESID 101:101 ) OR ( CHAIN X AND RESID 101:101 ) OR ( CHAIN B AND ( RESID 1:739 OR RESID 801:848 ) ) OR ( CHAIN M AND RESID 1201:1201 )B801 - 848
8X-RAY DIFFRACTION2( CHAIN I AND RESID 101:101 ) OR ( CHAIN X AND RESID 101:101 ) OR ( CHAIN B AND ( RESID 1:739 OR RESID 801:848 ) ) OR ( CHAIN M AND RESID 1201:1201 )M1201
9X-RAY DIFFRACTION3( CHAIN C AND ( RESID 1:80 OR RESID 101:102 ) )C1 - 80
10X-RAY DIFFRACTION3( CHAIN C AND ( RESID 1:80 OR RESID 101:102 ) )C101 - 102
11X-RAY DIFFRACTION4( CHAIN D AND RESID 1:138 )D1 - 138
12X-RAY DIFFRACTION5( CHAIN E AND RESID 1:69 )E1 - 69
13X-RAY DIFFRACTION6( CHAIN F AND ( RESID 1:141 OR RESID 1301:1302 ) )F1 - 141
14X-RAY DIFFRACTION6( CHAIN F AND ( RESID 1:141 OR RESID 1301:1302 ) )F1301 - 1302
15X-RAY DIFFRACTION7( CHAIN I AND ( RESID 1:38 OR RESID 102:102 ) ) OR ( CHAIN B AND RESID 849:849 )I1 - 38
16X-RAY DIFFRACTION7( CHAIN I AND ( RESID 1:38 OR RESID 102:102 ) ) OR ( CHAIN B AND RESID 849:849 )I102
17X-RAY DIFFRACTION7( CHAIN I AND ( RESID 1:38 OR RESID 102:102 ) ) OR ( CHAIN B AND RESID 849:849 )B849
18X-RAY DIFFRACTION8( CHAIN B AND RESID 850:850 ) OR ( CHAIN J AND ( RESID 1:41 OR RESID 1102:1105 ) )B850
19X-RAY DIFFRACTION8( CHAIN B AND RESID 850:850 ) OR ( CHAIN J AND ( RESID 1:41 OR RESID 1102:1105 ) )J1 - 41
20X-RAY DIFFRACTION8( CHAIN B AND RESID 850:850 ) OR ( CHAIN J AND ( RESID 1:41 OR RESID 1102:1105 ) )J1102 - 1105
21X-RAY DIFFRACTION9( CHAIN K AND RESID 20:77 ) OR ( CHAIN A AND RESID 855)K20 - 77
22X-RAY DIFFRACTION9( CHAIN K AND RESID 20:77 ) OR ( CHAIN A AND RESID 855)A855
23X-RAY DIFFRACTION10( CHAIN L AND ( RESID 4:154 OR RESID 1001:1006 ) )L4 - 154
24X-RAY DIFFRACTION10( CHAIN L AND ( RESID 4:154 OR RESID 1001:1006 ) )L1001 - 1006
25X-RAY DIFFRACTION11( CHAIN M AND ( RESID 1:31 OR RESID 1202:1203 ) )M1 - 31
26X-RAY DIFFRACTION11( CHAIN M AND ( RESID 1:31 OR RESID 1202:1203 ) )M1202 - 1203
27X-RAY DIFFRACTION12( CHAIN X AND ( RESID 7:35 OR RESID 102:102 ) )X7 - 35
28X-RAY DIFFRACTION12( CHAIN X AND ( RESID 7:35 OR RESID 102:102 ) )X102

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