Journal: PLoS Biol / Year: 2010 Title: Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. Authors: Natacha Opalka / Jesse Brown / William J Lane / Kelly-Anne F Twist / Robert Landick / Francisco J Asturias / Seth A Darst / Abstract: The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the ...The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program.
Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 24, 2009
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9919 Å / Relative weight: 1
Reflection
Resolution: 1.6→25 Å / Num. obs: 42737 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.069 / Net I/σ(I): 40
Reflection shell
Resolution: 1.6→1.64 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.416 / % possible all: 94
-
Processing
Software
Name
Version
Classification
MAR345dtb
datacollection
SHARP
phasing
REFMAC
5.5.0091
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.6→14.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.653 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22955
1398
3.2 %
RANDOM
Rwork
0.20791
-
-
-
obs
0.20884
42737
98.5 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 11.586 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.02 Å2
0 Å2
0 Å2
2-
-
-0.55 Å2
0 Å2
3-
-
-
-0.47 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→14.98 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2317
0
0
378
2695
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
2397
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1685
X-RAY DIFFRACTION
r_angle_refined_deg
1.134
2.01
3243
X-RAY DIFFRACTION
r_angle_other_deg
0.812
3
4095
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.059
5
296
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.549
23.852
122
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.373
15
411
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.423
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.062
0.2
369
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
2636
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
491
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
0.514
1.5
1435
X-RAY DIFFRACTION
r_mcbond_other
0.083
1.5
578
X-RAY DIFFRACTION
r_mcangle_it
0.983
2
2331
X-RAY DIFFRACTION
r_scbond_it
1.435
3
962
X-RAY DIFFRACTION
r_scangle_it
2.456
4.5
905
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.6→1.642 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rwork
0.249
3118
-
Rfree
-
0
-
obs
-
-
100 %
+
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