2NVX

RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-11% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.6566.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.719α = 90
b = 222.414β = 101.29
c = 193.071γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.65093.10.1349.22.880737-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.63.7393.90.72922.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1SFO3.65070160372191.530.28560.284610.30403RANDOM110.055
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]
1.94-1.68-2.11-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.701
r_dihedral_angle_3_deg18.923
r_dihedral_angle_4_deg15.18
r_dihedral_angle_1_deg7.629
r_scangle_it2.129
r_angle_refined_deg1.441
r_scbond_it1.43
r_mcangle_it1.022
r_mcbond_it0.77
r_symmetry_hbond_refined0.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.701
r_dihedral_angle_3_deg18.923
r_dihedral_angle_4_deg15.18
r_dihedral_angle_1_deg7.629
r_scangle_it2.129
r_angle_refined_deg1.441
r_scbond_it1.43
r_mcangle_it1.022
r_mcbond_it0.77
r_symmetry_hbond_refined0.365
r_nbtor_refined0.311
r_nbd_refined0.286
r_symmetry_vdw_refined0.272
r_xyhbond_nbd_refined0.235
r_chiral_restr0.222
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28305
Nucleic Acid Atoms1066
Solvent Atoms
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement