3S1N

RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NVQPDB ENTRY 2NVQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6293390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.4564.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.303α = 90
b = 221.128β = 97.52
c = 191.935γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2010-02-26MSINGLE 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 Merge 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
13.1501000.1196.93.8119031
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.211000.7293.711842

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 2NVQ3.147.811887059600.19260.19050.2323RANDOM92.8508
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]
-22.390214.32753.372719.0174
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion22.07
t_omega_torsion2.44
t_angle_deg1.18
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion22.07
t_omega_torsion2.44
t_angle_deg1.18
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28292
Nucleic Acid Atoms269
Solvent Atoms
Heterogen Atoms9

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement