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12-Subunit RNA Polymerase II Refined with Zn-SAD data
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B8K PDB ENTRY 2B8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 5-7% PEG 4000, 50 mM HEPES pH 7.0, 10 mM DTT, 70 mM glucosamine, 50 mM dioxane, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 5.89 79.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.581 α = 90 b = 391.537 β = 90 c = 280.734 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2004-11-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 3.8 25 107033
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2B8K 3.88 20.22 100869 5314 95.5 0.283 0.282 0.301 0.2488 RANDOM 110.463
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] -1.48 -0.96 2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.808 r_dihedral_angle_3_deg 15.646 r_dihedral_angle_4_deg 10.461 r_dihedral_angle_1_deg 4.244 r_angle_other_deg 1.285 r_angle_refined_deg 0.855 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.808 r_dihedral_angle_3_deg 15.646 r_dihedral_angle_4_deg 10.461 r_dihedral_angle_1_deg 4.244 r_angle_other_deg 1.285 r_angle_refined_deg 0.855 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31403 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling