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- PDB-2pmz: Archaeal RNA polymerase from Sulfolobus solfataricus -

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Basic information

Entry
Database: PDB / ID: 2pmz
TitleArchaeal RNA polymerase from Sulfolobus solfataricus
Components(DNA-directed RNA polymerase subunit ...) x 11
KeywordsTRANSLATION / TRANSFERASE / 4Fe-4S cluster binding motif
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / transcription by RNA polymerase I / tRNA transcription by RNA polymerase III / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II / protein dimerization activity ...3 iron, 4 sulfur cluster binding / transcription by RNA polymerase I / tRNA transcription by RNA polymerase III / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA polymerase; domain 1 - #390 / DNA-directed RNA polymerase subunit Rpo4 / Dihydrolipoamide Transferase / DNA-directed RNA polymerase subunit Rpo12 ...Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA polymerase; domain 1 - #390 / DNA-directed RNA polymerase subunit Rpo4 / Dihydrolipoamide Transferase / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo7 / HRDC domain / RNA polymerase ii / RNA polymerase Rpb1 funnel domain / N-terminal domain of TfIIb / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Other non-globular / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Rubrerythrin, domain 2 / Helix Hairpins / Gyrase A; domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / : / Homeodomain-like / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Single Sheet / S1 domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Beta Complex / Helix non-globular / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3
Similarity search - Domain/homology
FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1N ...FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo4
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMurakami, K.S.
CitationJournal: Nature / Year: 2008
Title: The X-ray crystal structure of RNA polymerase from Archaea
Authors: Hirata, A. / Klein, B.J. / Murakami, K.S.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit A
C: DNA-directed RNA polymerase subunit A"
B: DNA-directed RNA polymerase subunit B
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase subunit E
F: DNA-directed RNA polymerase subunit F
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
Q: DNA-directed RNA polymerase subunit A
G: DNA-directed RNA polymerase subunit A"
R: DNA-directed RNA polymerase subunit B
S: DNA-directed RNA polymerase subunit D
T: DNA-directed RNA polymerase subunit E
U: DNA-directed RNA polymerase subunit F
V: DNA-directed RNA polymerase subunit H
W: DNA-directed RNA polymerase subunit K
X: DNA-directed RNA polymerase subunit L
Y: DNA-directed RNA polymerase subunit N
Z: DNA-directed RNA polymerase subunit P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)756,48934
Polymers755,32522
Non-polymers1,16312
Water00
1
A: DNA-directed RNA polymerase subunit A
C: DNA-directed RNA polymerase subunit A"
B: DNA-directed RNA polymerase subunit B
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase subunit E
F: DNA-directed RNA polymerase subunit F
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,24417
Polymers377,66311
Non-polymers5826
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: DNA-directed RNA polymerase subunit A
G: DNA-directed RNA polymerase subunit A"
R: DNA-directed RNA polymerase subunit B
S: DNA-directed RNA polymerase subunit D
T: DNA-directed RNA polymerase subunit E
U: DNA-directed RNA polymerase subunit F
V: DNA-directed RNA polymerase subunit H
W: DNA-directed RNA polymerase subunit K
X: DNA-directed RNA polymerase subunit L
Y: DNA-directed RNA polymerase subunit N
Z: DNA-directed RNA polymerase subunit P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,24417
Polymers377,66311
Non-polymers5826
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.820, 201.235, 196.050
Angle α, β, γ (deg.)90.000, 100.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21Q
12B
22R
13C
23G
14D
24S
15E
25T
16F
26U
17H
27V
18K
28W
19L
29X
110N
210Y
111P
211Z

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSMGAA - X4 - 10034 - 1
21LYSMGQL - CA4 - 10034 - 1
12LEUZNBC - Y5 - 20015 - 1
22LEUZNRN - DA5 - 20015 - 1
13PROARGCB11 - 3958 - 392
23PROARGGM11 - 3958 - 392
14SERF3SDD - GA2 - 10012 - 1
24SERF3SSO - HA2 - 10012 - 1
15METLYSEE1 - 1801 - 180
25METLYSTP1 - 1801 - 180
16METMETFF1 - 891 - 89
26METMETUQ1 - 891 - 89
17ILEILEHG9 - 829 - 82
27ILEILEVR9 - 829 - 82
18GLNLEUKH11 - 9211 - 92
28GLNLEUWS11 - 9211 - 92
19METLYSLI1 - 921 - 92
29METLYSXT1 - 921 - 92
110METZNNJ - Z1 - 10011
210METZNYU - EA1 - 10011
111CYSZNPK - AA6 - 10016 - 1
211CYSZNZV - FA6 - 10016 - 1

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

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Components

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DNA-directed RNA polymerase subunit ... , 11 types, 22 molecules AQCGBRDSETFUHVKWLXNYPZ

#1: Protein DNA-directed RNA polymerase subunit A / E.C.2.7.7.6


Mass: 99815.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980R2, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit A" / E.C.2.7.7.6


Mass: 43548.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: P58192, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit B / E.C.2.7.7.6


Mass: 126721.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980R1, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit D / E.C.2.7.7.6


Mass: 30330.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: P95989, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit E / E.C.2.7.7.6


Mass: 20354.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980A3, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase subunit F / E.C.2.7.7.6


Mass: 12825.573 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q9UXD9, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase subunit H / E.C.2.7.7.6


Mass: 9687.307 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980Q9, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit K / E.C.2.7.7.6


Mass: 10871.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q97ZJ9, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit L / E.C.2.7.7.6


Mass: 10298.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980K0, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit N / E.C.2.7.7.6


Mass: 7602.009 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q980Z8, DNA-directed RNA polymerase
#11: Protein/peptide DNA-directed RNA polymerase subunit P / E.C.2.7.7.6


Mass: 5606.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus solfataricus (archaea) / Strain: P2 / References: UniProt: Q97ZX7, DNA-directed RNA polymerase

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Non-polymers , 3 types, 12 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#14: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4

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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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes (pH 7.5), 0.1 M K2CO3, 0.1M Na2S203, 12%(w/v) PEG10000, 2mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 28, 2005 / Details: Osmic confocal blue optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 105621 / % possible obs: 80.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.097 / Χ2: 1.284 / Net I/σ(I): 10.3
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 1.54 / Num. unique all: 7294 / Χ2: 1.124 / % possible all: 55.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.4 Å39.79 Å
Translation3.4 Å39.79 Å
Phasing dmFOM centric: 0.7 / Reflection centric: 2138
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.7-39.7910.930.930.8851064802304
6.1-9.70.830.830.781604415538506
4.9-6.10.750.750.711931018902408
4.3-4.90.760.760.731876718444323
3.6-4.30.590.590.593089730435462
3.4-3.60.30.30.271549215357135

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.12phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→39.79 Å / Cor.coef. Fo:Fc: 0.822 / Cor.coef. Fo:Fc free: 0.716 / Rfactor Rfree error: 0.005 / SU B: 63.295 / SU ML: 1.007 / Data cutoff high absF: 6375810.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.985 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.343 5312 5 %RANDOM
Rwork0.2739 ---
all0.274 ---
obs0.274 105616 80.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8317 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 93.8 Å2
Baniso -1Baniso -2Baniso -3
1-8.86 Å20 Å2-17.75 Å2
2--7.29 Å20 Å2
3----16.15 Å2
Refinement stepCycle: LAST / Resolution: 3.4→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48098 0 24 0 48122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.00910.02248886
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.98266112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27856006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4823.6462172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.296158972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.57615412
X-RAY DIFFRACTIONr_chiral_restr0.1010.27540
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0236284
X-RAY DIFFRACTIONr_nbd_refined0.2690.228767
X-RAY DIFFRACTIONr_nbtor_refined0.3140.232335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.21790
X-RAY DIFFRACTIONr_metal_ion_refined0.2970.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.27
X-RAY DIFFRACTIONr_mcbond_it0.7421.530979
X-RAY DIFFRACTIONr_mcangle_it1.339248900
X-RAY DIFFRACTIONr_scbond_it1.052319453
X-RAY DIFFRACTIONr_scangle_it1.8354.517206
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A6175MEDIUM POSITIONAL0.290.5
1A6175MEDIUM THERMAL0.432
2B8595MEDIUM POSITIONAL0.280.5
2B8595MEDIUM THERMAL0.362
3C2168MEDIUM POSITIONAL0.310.5
3C2168MEDIUM THERMAL0.432
4D2121MEDIUM POSITIONAL0.320.5
4D2121MEDIUM THERMAL0.382
5E1400MEDIUM POSITIONAL0.340.5
5E1400MEDIUM THERMAL0.272
6F694MEDIUM POSITIONAL0.340.5
6F694MEDIUM THERMAL0.212
7H612MEDIUM POSITIONAL0.290.5
7H612MEDIUM THERMAL0.312
8K659MEDIUM POSITIONAL0.30.5
8K659MEDIUM THERMAL0.482
9L723MEDIUM POSITIONAL0.320.5
9L723MEDIUM THERMAL0.552
10N515MEDIUM POSITIONAL0.310.5
10N515MEDIUM THERMAL0.272
11P347MEDIUM POSITIONAL0.340.5
11P347MEDIUM THERMAL0.272
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 244 -
Rwork0.384 4995 -
obs-5239 54.64 %

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