☰ Navigation Tabs
RNA Polymerase II elongation complex with UTP, updated 11/2006
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, 9-12% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.82 67.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.647 α = 90 b = 222.338 β = 101.67 c = 194.316 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 CCD ADSC QUANTUM 4 2003-02-21 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 4.2 40 95.8 0.157 11.8 2.5 50043 -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) 4.2 4.3 93.2 0.361
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 4.3 40 37247 4179 0.27605 0.26983 0.277 0.33165 0.3295 RANDOM 126.993
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.073 r_dihedral_angle_3_deg 21.606 r_dihedral_angle_4_deg 17.847 r_dihedral_angle_1_deg 7.07 r_angle_refined_deg 1.364 r_scangle_it 0.973 r_mcangle_it 0.615 r_scbond_it 0.494 r_mcbond_it 0.34 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.073 r_dihedral_angle_3_deg 21.606 r_dihedral_angle_4_deg 17.847 r_dihedral_angle_1_deg 7.07 r_angle_refined_deg 1.364 r_scangle_it 0.973 r_mcangle_it 0.615 r_scbond_it 0.494 r_mcbond_it 0.34 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.299 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.223 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.098 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 27897 Nucleic Acid Atoms 1066 Solvent Atoms Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction