RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / mediator complex / termination of RNA polymerase II transcription / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding ...RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / mediator complex / termination of RNA polymerase II transcription / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to nutrient levels / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / transcription corepressor activity / protein-macromolecule adaptor activity / cellular response to heat / DNA-binding transcription factor binding / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function
Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med20 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex ...Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med20 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 11 Similarity search - Component
A: Mediator of RNA polymerase II transcription subunit 11 B: Mediator of RNA polymerase II transcription subunit 17 C: Mediator of RNA polymerase II transcription subunit 8 D: Mediator of RNA polymerase II transcription subunit 22 E: Mediator of RNA polymerase II transcription subunit 18 F: Mediator of RNA polymerase II transcription subunit 20 G: Mediator of RNA polymerase II transcription subunit 6
Resolution: 4.2→4.43 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / % possible all: 97.7
-
Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
SHARP
phasing
REFMAC
5.6.0117
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MIRAS / Resolution: 4.2→45 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.884 / SU B: 74.271 / SU ML: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.915 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.35709
1341
5 %
RANDOM
Rwork
0.29038
-
-
-
all
0.29366
26754
-
-
obs
0.29366
25254
99.27 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 162.713 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.06 Å2
2.53 Å2
0 Å2
2-
-
5.06 Å2
0 Å2
3-
-
-
-7.59 Å2
Refinement step
Cycle: LAST / Resolution: 4.2→45 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9033
0
0
0
9033
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.019
9093
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.616
1.956
12524
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.919
5
1529
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.743
24.877
162
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.274
15
693
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.916
15
19
X-RAY DIFFRACTION
r_chiral_restr
0.095
0.2
1638
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
7020
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 4.2→4.308 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.449
86
-
Rwork
0.371
1656
-
obs
-
-
97.05 %
+
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