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RNA polymerase II elongation complex at 5 mM Mg2+ with GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFO
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 3.72 66.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.108 α = 90 b = 222.005 β = 102.61 c = 195.163 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 2006-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 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 3.95 50 98.3 0.145 10.3 3.4 60760 -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) 3.95 4.09 92.2 0.465 2.3 2.9
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 1SFO 3.95 45.08 57635 3078 97.77 0.29421 0.29034 0.27 0.36755 0.3319 RANDOM 127.115
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] 0.01 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.436 r_dihedral_angle_3_deg 21.835 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_1_deg 11.961 r_angle_refined_deg 1.261 r_scangle_it 1.11 r_mcangle_it 0.725 r_scbond_it 0.585 r_mcbond_it 0.397 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.436 r_dihedral_angle_3_deg 21.835 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_1_deg 11.961 r_angle_refined_deg 1.261 r_scangle_it 1.11 r_mcangle_it 0.725 r_scbond_it 0.585 r_mcbond_it 0.397 r_nbtor_refined 0.314 r_nbd_refined 0.284 r_symmetry_vdw_refined 0.237 r_symmetry_hbond_refined 0.203 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.079 r_metal_ion_refined 0.017 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_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 27897 Nucleic Acid Atoms 1064 Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement