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Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K83 PDB ENTRY 1K83
Crystallization Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.51 α = 90 b = 222.48 β = 90 c = 374.23 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 20 124441
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1K83 2.8 20 112956 3507 93.4 0.202 0.2 0.2095 0.273 0.2773 RANDOM 33.1
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] 0.33 0.06 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.214 r_dihedral_angle_3_deg 21.707 r_dihedral_angle_4_deg 21.036 r_dihedral_angle_1_deg 8.942 r_scangle_it 2.984 r_angle_refined_deg 1.827 r_scbond_it 1.783 r_mcangle_it 1.393 r_mcbond_it 0.792 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.214 r_dihedral_angle_3_deg 21.707 r_dihedral_angle_4_deg 21.036 r_dihedral_angle_1_deg 8.942 r_scangle_it 2.984 r_angle_refined_deg 1.827 r_scbond_it 1.783 r_mcangle_it 1.393 r_mcbond_it 0.792 r_nbtor_refined 0.321 r_symmetry_hbond_refined 0.299 r_nbd_refined 0.256 r_symmetry_vdw_refined 0.226 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.139 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 27315 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement