4MQ9 | pdb_00004mq9

Crystal structure of Thermus thermophilus RNA polymerase holoenzyme in complex with GE23077

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DXJ	PDB ENTRY 3DXJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	295	A stock crystallization solution was prepared by adding T. thermophilus RNAP holoenzyme (10 mg/ml) in 20 mm TRIS-HCl, ph 7.7, 100 mm NaCl, and 1% glycerol to an equal volume of 33 mm magnesium formate containing 40 m ZnCl2. This solution was equilibrated against 35 mm magnesium formate and 30 mm sodium citrate, ph 5.4, vapor diffusion, hanging drop, temperature 295K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
4.75	74.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 236.569	α = 90
b = 236.569	β = 90
c = 252.311	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 270		2010-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91800	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.35	39.76	99.1	0.112	8.5428	5.81		113506		1.35

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.35	3.53	97.2		1	0.76	5.39

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3DXJ	3.35	38.971	1.35	113359	2265	98.9	0.2143	0.2138	0.21	0.242	0.24	156.78

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
16.5497			16.5497		-33.0994

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.777
f_angle_d	0.846
f_chiral_restr	0.062
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26543
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	5

Software

Software
Software Name	Purpose
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.