2E2I

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R9T 

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
3.6966.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.682α = 90
b = 223.524β = 100.54
c = 193.938γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002006-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
13.45098.30.14414.65.394186-3
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)
3.43.5290.80.56224.3

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 REPLACEMENTTHROUGHOUT1R9T3.415089433473297.970.268830.266350.31632RANDOM116.893
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]
4.42-7.2-3.25-3.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.909
r_dihedral_angle_3_deg19.852
r_dihedral_angle_4_deg14.699
r_dihedral_angle_1_deg8.144
r_scangle_it2.533
r_mcangle_it2.332
r_mcbond_it1.898
r_angle_refined_deg1.594
r_scbond_it1.429
r_symmetry_hbond_refined0.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.909
r_dihedral_angle_3_deg19.852
r_dihedral_angle_4_deg14.699
r_dihedral_angle_1_deg8.144
r_scangle_it2.533
r_mcangle_it2.332
r_mcbond_it1.898
r_angle_refined_deg1.594
r_scbond_it1.429
r_symmetry_hbond_refined0.334
r_nbtor_refined0.316
r_symmetry_vdw_refined0.276
r_nbd_refined0.259
r_xyhbond_nbd_refined0.184
r_chiral_restr0.102
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 Atoms28587
Nucleic Acid Atoms1064
Solvent Atoms
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement