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Basic information

Entry
Database: PDB / ID: 3i9v
TitleCrystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 2 mol/ASU
Components(NADH-quinone oxidoreductase subunit ...) x 8
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / RESPIRATORY CHAIN / Cell membrane / Flavoprotein / FMN / Iron / Iron-sulfur / Membrane / Metal-binding / NAD / Quinone / Disulfide bond / Transport
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / iron-sulfur cluster assembly / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / ferric iron binding / 2 iron, 2 sulfur cluster binding ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / iron-sulfur cluster assembly / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / ferric iron binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase subunit E / Alpha-Beta Plaits - #3270 / NADH-quinone oxidoreductase, subunit 15 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily ...NADH-quinone oxidoreductase subunit E / Alpha-Beta Plaits - #3270 / NADH-quinone oxidoreductase, subunit 15 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily / Soluble ligand binding domain / de novo design (two linked rop proteins) / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / 2Fe-2S iron-sulfur cluster binding domain / Cro/C1-type helix-turn-helix domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / Aspartate decarboxylase-like domain superfamily / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Thioredoxin-like [2Fe-2S] ferredoxin / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like 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 / Helix non-globular / Special / Glutaredoxin / Glutaredoxin / Ubiquitin-like (UB roll) / Arc Repressor Mutant, subunit A / Thioredoxin-like superfamily / Alpha-Beta Plaits / Roll / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 15
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsSazanov, L.A. / Berrisford, J.M.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Structural basis for the mechanism of respiratory complex I
Authors: Berrisford, J.M. / Sazanov, L.A.
#1: Journal: Science / Year: 2006
Title: Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
Authors: Sazanov, L.A. / Hinchliffe, P.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit 5
6: NADH-quinone oxidoreductase subunit 6
9: NADH-quinone oxidoreductase subunit 9
7: NADH-quinone oxidoreductase subunit 15
A: NADH-quinone oxidoreductase subunit 1
B: NADH-quinone oxidoreductase subunit 2
C: NADH-quinone oxidoreductase subunit 3
D: NADH-quinone oxidoreductase subunit 4
E: NADH-quinone oxidoreductase subunit 5
F: NADH-quinone oxidoreductase subunit 6
G: NADH-quinone oxidoreductase subunit 9
H: NADH-quinone oxidoreductase subunit 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)569,60150
Polymers562,32316
Non-polymers7,27834
Water00
1
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit 5
6: NADH-quinone oxidoreductase subunit 6
9: NADH-quinone oxidoreductase subunit 9
7: NADH-quinone oxidoreductase subunit 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,85526
Polymers281,1618
Non-polymers3,69418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38680 Å2
ΔGint-381 kcal/mol
Surface area81990 Å2
MethodPISA
2
A: NADH-quinone oxidoreductase subunit 1
B: NADH-quinone oxidoreductase subunit 2
C: NADH-quinone oxidoreductase subunit 3
D: NADH-quinone oxidoreductase subunit 4
E: NADH-quinone oxidoreductase subunit 5
F: NADH-quinone oxidoreductase subunit 6
G: NADH-quinone oxidoreductase subunit 9
H: NADH-quinone oxidoreductase subunit 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,74624
Polymers281,1618
Non-polymers3,58416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38290 Å2
ΔGint-369 kcal/mol
Surface area82190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.963, 150.514, 216.726
Angle α, β, γ (deg.)90.000, 92.190, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
113
21C
121
22A
134
23D
145
24E
152
25B
169
26G
176
27F
187
28H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPROPROchain 3 and (resseq 1:55 or resseq 73:143 or resseq 150:777 )3C1 - 551 - 55
121ILEILETYRTYRchain 3 and (resseq 1:55 or resseq 73:143 or resseq 150:777 )3C73 - 14373 - 143
131GLUGLUVALVALchain 3 and (resseq 1:55 or resseq 73:143 or resseq 150:777 )3C150 - 777150 - 777
211METMETPROPROchain C and (resseq 1:55 or resseq 73:143 or resseq 150:777 )CK1 - 551 - 55
221ILEILETYRTYRchain C and (resseq 1:55 or resseq 73:143 or resseq 150:777 )CK73 - 14373 - 143
231GLUGLUVALVALchain C and (resseq 1:55 or resseq 73:143 or resseq 150:777 )CK150 - 777150 - 777
112THRTHRARGARGchain 1 and (resseq 2:438 )1A2 - 4382 - 438
212THRTHRARGARGchain A and (resseq 2:438 )AI2 - 4382 - 438
113METMETGLYGLYchain 4 and (resseq 26:31 or resseq 39:409 )4D26 - 3126 - 31
123GLYGLYARGARGchain 4 and (resseq 26:31 or resseq 39:409 )4D39 - 40939 - 409
213METMETGLYGLYchain D and (resseq 26:31 or resseq 39:409 )DL26 - 3126 - 31
223GLYGLYARGARGchain D and (resseq 26:31 or resseq 39:409 )DL39 - 40939 - 409
114METMETTRPTRPchain 5 and (resseq 1:196 )5E1 - 1961 - 196
214METMETTRPTRPchain E and (resseq 1:196 )EM1 - 1961 - 196
115PHEPHEGLUGLUchain 2 and (resseq 3:180 )2B3 - 1803 - 180
215PHEPHEGLUGLUchain B and (resseq 3:180 )BJ3 - 1803 - 180
116TYRTYRGLYGLYchain 9 and (resseq 26:179 )9G26 - 17926 - 179
216TYRTYRGLYGLYchain G and (resseq 26:179 )GO26 - 17926 - 179
117GLUGLUARGARGchain 6 and (resseq 15:57 or resseq 74:175 )6F15 - 5715 - 57
127GLNGLNALAALAchain 6 and (resseq 15:57 or resseq 74:175 )6F74 - 17574 - 175
217GLUGLUARGARGchain F and (resseq 15:57 or resseq 74:175 )FN15 - 5715 - 57
227GLNGLNALAALAchain F and (resseq 15:57 or resseq 74:175 )FN74 - 17574 - 175
118ALAALAALAALAchain 7 and (resseq 3:129 )7H3 - 1293 - 129
218ALAALAALAALAchain H and (resseq 3:129 )HP3 - 1293 - 129

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

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NADH-quinone oxidoreductase subunit ... , 8 types, 16 molecules 1A2B3C4D5E6F9G7H

#1: Protein NADH-quinone oxidoreductase subunit 1 / NADH dehydrogenase I chain 1 / NDH-1 subunit 1


Mass: 48693.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56222, NADH dehydrogenase (quinone)
#2: Protein NADH-quinone oxidoreductase subunit 2 / NADH dehydrogenase I chain 2 / NDH-1 subunit 2


Mass: 20309.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56221, NADH dehydrogenase (quinone)
#3: Protein NADH-quinone oxidoreductase subunit 3 / NADH dehydrogenase I chain 3 / NDH-1 subunit 3


Mass: 86656.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56223, NADH dehydrogenase (quinone)
#4: Protein NADH-quinone oxidoreductase subunit 4 / NADH dehydrogenase I chain 4 / NDH-1 subunit 4


Mass: 46428.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56220, NADH dehydrogenase (quinone)
#5: Protein NADH-quinone oxidoreductase subunit 5 / NADH dehydrogenase I chain 5 / NDH-1 subunit 5


Mass: 23893.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56219, NADH dehydrogenase (quinone)
#6: Protein NADH-quinone oxidoreductase subunit 6 / NADH dehydrogenase I subunit 6 / NDH-1 subunit 6


Mass: 20262.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56218, NADH dehydrogenase (quinone)
#7: Protein NADH-quinone oxidoreductase subunit 9 / NADH dehydrogenase I subunit 9 / NDH-1 subunit 9


Mass: 20106.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56224, NADH dehydrogenase (quinone)
#8: Protein NADH-quinone oxidoreductase subunit 15 / NADH dehydrogenase I chain 15 / NDH-1 subunit 15


Mass: 14812.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SKZ7, NADH dehydrogenase (quinone)

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Non-polymers , 5 types, 34 molecules

#9: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#11: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#12: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#13: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.4 M NaCl, 0.1 M MnCl2, 6% PEG4000, 2.5% PEG400, 20 mM NAD+, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2007
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 102553 / Num. obs: 102553 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 62.24 Å2 / Rmerge(I) obs: 0.138 / Rsym value: 0.138 / Net I/σ(I): 5.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 1.2 / Num. unique all: 15411 / Rsym value: 0.538 / % possible all: 84.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FUG

2fug


Resolution: 3.1→29.935 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.773 / SU ML: 0.57 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1838 1.79 %Random
Rwork0.235 ---
all0.236 102544 --
obs0.236 102544 81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.297 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 152.74 Å2 / Biso mean: 64.94 Å2 / Biso min: 18.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.665 Å20 Å210.97 Å2
2---16.088 Å20 Å2
3---13.189 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37316 0 204 0 37520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00938592
X-RAY DIFFRACTIONf_angle_d1.39352608
X-RAY DIFFRACTIONf_chiral_restr0.0845654
X-RAY DIFFRACTIONf_plane_restr0.0076798
X-RAY DIFFRACTIONf_dihedral_angle_d21.87214336
X-RAY DIFFRACTIONf_b_iso_bonded_d5.32
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
1135881X-RAY DIFFRACTIONPOSITIONAL0.034
12C5881X-RAY DIFFRACTIONPOSITIONAL0.034
2113417X-RAY DIFFRACTIONPOSITIONAL0.037
22A3417X-RAY DIFFRACTIONPOSITIONAL0.037
3143011X-RAY DIFFRACTIONPOSITIONAL0.031
32D3011X-RAY DIFFRACTIONPOSITIONAL0.031
4151608X-RAY DIFFRACTIONPOSITIONAL0.03
42E1608X-RAY DIFFRACTIONPOSITIONAL0.03
5121407X-RAY DIFFRACTIONPOSITIONAL0.035
52B1407X-RAY DIFFRACTIONPOSITIONAL0.035
6191194X-RAY DIFFRACTIONPOSITIONAL0.037
62G1194X-RAY DIFFRACTIONPOSITIONAL0.037
7161114X-RAY DIFFRACTIONPOSITIONAL0.034
72F1114X-RAY DIFFRACTIONPOSITIONAL0.034
8171031X-RAY DIFFRACTIONPOSITIONAL0.032
82H1031X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3.1-3.2630.3572540.33914773150271477384
3.263-3.4670.352700.31414750150201475083
3.467-3.7350.3273010.27814665149661466583
3.735-4.110.2982670.23514569148361456982
4.11-4.7020.2442660.19714458147241445881
4.702-5.9170.2482310.19114126143571412679
5.917-29.9360.2322490.19713365136141336574

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