2E2J

RNA polymerase II elongation complex in 5 mM Mg+2 with GMPCPP


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
Matthew coefficientSolvent content
3.7166.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.142α = 90
b = 222.017β = 101.36
c = 194.652γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002005-11-01MSINGLE 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
13.55095.40.18610.28.284357-3
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)
3.53.6381.30.5331.33.8

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 REPLACEMENTTHROUGHOUT1SFO3.55081551251194.510.244010.242150.30602RANDOM106.188
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]
2.81-7.56-3.65-2.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.507
r_dihedral_angle_3_deg20.606
r_dihedral_angle_4_deg16.904
r_dihedral_angle_1_deg6.507
r_scangle_it1.997
r_angle_refined_deg1.492
r_mcangle_it1.225
r_scbond_it1.134
r_mcbond_it0.679
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.507
r_dihedral_angle_3_deg20.606
r_dihedral_angle_4_deg16.904
r_dihedral_angle_1_deg6.507
r_scangle_it1.997
r_angle_refined_deg1.492
r_mcangle_it1.225
r_scbond_it1.134
r_mcbond_it0.679
r_nbtor_refined0.314
r_metal_ion_refined0.26
r_symmetry_vdw_refined0.256
r_nbd_refined0.244
r_xyhbond_nbd_refined0.175
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_sphericity_bonded
r_metal_ion_other
r_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_gen_planes_other
r_bond_other_d
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28153
Nucleic Acid Atoms1011
Solvent Atoms
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement