3CQZ

Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K83PDB ENTRY 1K83

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.7154.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.51α = 90
b = 222.48β = 90
c = 374.23γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.820124441

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 1K832.820112956350793.40.2020.20.273RANDOM33.1
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]
0.330.06-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.214
r_dihedral_angle_3_deg21.707
r_dihedral_angle_4_deg21.036
r_dihedral_angle_1_deg8.942
r_scangle_it2.984
r_angle_refined_deg1.827
r_scbond_it1.783
r_mcangle_it1.393
r_mcbond_it0.792
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.214
r_dihedral_angle_3_deg21.707
r_dihedral_angle_4_deg21.036
r_dihedral_angle_1_deg8.942
r_scangle_it2.984
r_angle_refined_deg1.827
r_scbond_it1.783
r_mcangle_it1.393
r_mcbond_it0.792
r_nbtor_refined0.321
r_symmetry_hbond_refined0.299
r_nbd_refined0.256
r_symmetry_vdw_refined0.226
r_xyhbond_nbd_refined0.163
r_chiral_restr0.139
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 Atoms27315
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement