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RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP
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 7 298 200mM NH4OAc, 150mM Mg(OAc)2, 50mM Hepes, pH 7.0, 5% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.74 67.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.646 α = 90 b = 222.76 β = 101.31 c = 195.281 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 CCD ADSC QUANTUM 315 2004-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.00 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 2.9 48.45 98.9 0.142 8.1 3.2 146322 -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) 1 3 3.1 94.9 0.746 1.4 2.4
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 2.9 48.45 141295 4429 92.74 0.23 0.229 0.2622 0.283 0.3012 RANDOM 59.84
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] 0.14 -0.4 -0.37 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.609 r_dihedral_angle_3_deg 21.37 r_dihedral_angle_4_deg 18.729 r_dihedral_angle_1_deg 6.998 r_scangle_it 3.235 r_scbond_it 1.993 r_angle_refined_deg 1.875 r_mcangle_it 1.503 r_mcbond_it 0.849 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.609 r_dihedral_angle_3_deg 21.37 r_dihedral_angle_4_deg 18.729 r_dihedral_angle_1_deg 6.998 r_scangle_it 3.235 r_scbond_it 1.993 r_angle_refined_deg 1.875 r_mcangle_it 1.503 r_mcbond_it 0.849 r_nbtor_refined 0.322 r_symmetry_hbond_refined 0.263 r_nbd_refined 0.252 r_symmetry_vdw_refined 0.236 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.127 r_metal_ion_refined 0.049 r_bond_refined_d 0.018 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28292 Nucleic Acid Atoms 1066 Solvent Atoms Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing