4MQ9

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DXJPDB ENTRY 3DXJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4295A 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 coefficientSolvent content
4.7574.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 236.569α = 90
b = 236.569β = 90
c = 252.311γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702010-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.91800CHESSF1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.3539.7699.10.1128.54285.811135061.35
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.353.5397.210.765.39

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3DXJ3.3538.9711.35113359226598.90.21430.21380.242156.78
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]
16.549716.5497-33.0994
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.777
f_angle_d0.846
f_chiral_restr0.062
f_bond_d0.004
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26543
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms5

Software

Software
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing