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RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-11% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.69 66.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.682 α = 90 b = 223.524 β = 100.54 c = 193.938 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2006-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 3.4 50 98.3 0.144 14.6 5.3 94186 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.4 3.52 90.8 0.562 2 4.3
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 1R9T 3.41 50 89433 4732 97.97 0.26883 0.26635 0.2565 0.31632 0.2998 RANDOM 116.893
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] 4.42 -7.2 -3.25 -3.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.909 r_dihedral_angle_3_deg 19.852 r_dihedral_angle_4_deg 14.699 r_dihedral_angle_1_deg 8.144 r_scangle_it 2.533 r_mcangle_it 2.332 r_mcbond_it 1.898 r_angle_refined_deg 1.594 r_scbond_it 1.429 r_symmetry_hbond_refined 0.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.909 r_dihedral_angle_3_deg 19.852 r_dihedral_angle_4_deg 14.699 r_dihedral_angle_1_deg 8.144 r_scangle_it 2.533 r_mcangle_it 2.332 r_mcbond_it 1.898 r_angle_refined_deg 1.594 r_scbond_it 1.429 r_symmetry_hbond_refined 0.334 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.259 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.102 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 28587 Nucleic Acid Atoms 1064 Solvent Atoms Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement