3M4O

RNA polymerase II elongation complex B


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298390mM (NH4)2HPO4/NaH2PO4, 50mM dioxane, 10mM DTT, 9-11% PEG6,000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.6266.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.114α = 90
b = 222.131β = 100.99
c = 191.782γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARMOSAIC 325 mm CCD2008-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.979SSRLBL11-1

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
13.574092.30.1666.32.57414470340
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)
3.573.6692.70.7161.42.3

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 REPLACEMENTTHROUGHOUTpdb entry 1R9T3.574070340368190.50.243910.241380.29233RANDOM130.199
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]
1.69-2.21-1.65-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.565
r_dihedral_angle_3_deg23.706
r_dihedral_angle_4_deg20.522
r_dihedral_angle_1_deg7.611
r_scangle_it1.899
r_angle_refined_deg1.568
r_mcangle_it1.116
r_scbond_it1.054
r_mcbond_it0.613
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.565
r_dihedral_angle_3_deg23.706
r_dihedral_angle_4_deg20.522
r_dihedral_angle_1_deg7.611
r_scangle_it1.899
r_angle_refined_deg1.568
r_mcangle_it1.116
r_scbond_it1.054
r_mcbond_it0.613
r_chiral_restr0.105
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms28140
Nucleic Acid Atoms1069
Solvent Atoms
Heterogen Atoms18

Software

Software
Software NamePurpose
HKL-2000data collection
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling