RNA polymerase II complex recruiting activity / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / TFIIH-class transcription factor complex binding / mediator complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping ...RNA polymerase II complex recruiting activity / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / TFIIH-class transcription factor complex binding / mediator complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase II transcription / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / TFIID-class transcription factor complex binding / Estrogen-dependent gene expression / Dual incision in TC-NER / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II, core complex / translesion synthesis / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / cytoplasmic stress granule / DNA-directed RNA polymerase / transcription corepressor activity / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / transcription by RNA polymerase II / 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 / mitochondrion / DNA binding / nucleus / metal ion binding Similarity search - Function
DNA-directed RNA polymerase II subunit RPB1 / 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 H: DNA-directed RNA polymerase II subunit RPB1
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 26, 2010
Radiation
Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 4.5→123.365 Å / Num. obs: 21971 / % possible obs: 99.8 % / Observed criterion σ(I): -3
Reflection shell
Resolution: 4.5→4.7 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 4.5 / % possible all: 100
-
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: 4.5→45 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.882 / SU B: 86.206 / SU ML: 1.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.345
1130
5.1 %
RANDOM
Rwork
0.286
-
-
-
obs
0.289
20920
99.9 %
-
all
-
21985
-
-
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: 181.17 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.22 Å2
2.11 Å2
0 Å2
2-
-
4.22 Å2
0 Å2
3-
-
-
-6.33 Å2
Refinement step
Cycle: LAST / Resolution: 4.5→45 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9217
0
0
0
9217
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.019
9287
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.56
1.957
12794
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.581
5
1553
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.397
24.759
166
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.831
15
711
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.546
15
19
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
1666
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
7172
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: 4.5→4.62 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.41
87
-
Rwork
0.385
1357
-
obs
-
-
99.59 %
+
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