2NVZ

RNA Polymerase II elongation complex with UTP, updated 11/2006


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.8267.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.647α = 90
b = 222.338β = 101.67
c = 194.316γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.98SSRLBL11-1

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
14.24095.80.15711.82.550043-3
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)
4.24.393.20.361

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 REPLACEMENTTHROUGHOUT1SFO4.3403724741790.276050.269830.33165RANDOM126.993
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.073
r_dihedral_angle_3_deg21.606
r_dihedral_angle_4_deg17.847
r_dihedral_angle_1_deg7.07
r_angle_refined_deg1.364
r_scangle_it0.973
r_mcangle_it0.615
r_scbond_it0.494
r_mcbond_it0.34
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.073
r_dihedral_angle_3_deg21.606
r_dihedral_angle_4_deg17.847
r_dihedral_angle_1_deg7.07
r_angle_refined_deg1.364
r_scangle_it0.973
r_mcangle_it0.615
r_scbond_it0.494
r_mcbond_it0.34
r_nbtor_refined0.307
r_symmetry_hbond_refined0.299
r_nbd_refined0.245
r_symmetry_vdw_refined0.223
r_xyhbond_nbd_refined0.177
r_chiral_restr0.098
r_bond_refined_d0.009
r_gen_planes_refined0.003
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 Atoms27897
Nucleic Acid Atoms1066
Solvent Atoms
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction