4X6A

Crystal structure of yeast RNA polymerase II encountering oxidative Cyclopurine DNA lesions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.15390 mM (NH4)2HPO4/NaH2PO4, PH 5.9-6.3, 50 mM dioxane, 10 mM DTT, and 10.7% - 11.6% PEG6000
Crystal Properties
Matthews coefficientSolvent content
3.4163.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.55α = 90
b = 220.334β = 97
c = 191.563γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
13.955098.40.2550.2710.123.45.154937
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.954.0297.70.9370.4550.7794.72692

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.965047410256088.950.25130.24890.2964RANDOM147.355
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]
25.4-13.07-6.23-15.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.9
r_dihedral_angle_3_deg24.242
r_dihedral_angle_4_deg19.886
r_mcangle_it10.227
r_dihedral_angle_1_deg9.224
r_mcbond_it6.023
r_mcbond_other6.023
r_angle_other_deg3.67
r_angle_refined_deg1.484
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.9
r_dihedral_angle_3_deg24.242
r_dihedral_angle_4_deg19.886
r_mcangle_it10.227
r_dihedral_angle_1_deg9.224
r_mcbond_it6.023
r_mcbond_other6.023
r_angle_other_deg3.67
r_angle_refined_deg1.484
r_chiral_restr0.084
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28121
Nucleic Acid Atoms419
Solvent Atoms
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement
Cootmodel building