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Crystal structure of elongating yeast RNA polymerase II stalled at oxidative Cyclopurine DNA lesions.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 390 mM (NH4)2HPO4/NaH2PO4, PH 5.9-6.3, 50 mM dioxane, 10 mM DTT, and 10.7% - 11.6% PEG6000
Crystal Properties Matthews coefficient Solvent content 3.66 66.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.146 α = 90 b = 220.798 β = 100.25 c = 193.919 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 315r 2013-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 4.1 50 86 0.222 0.27 0.152 3.6 2.7 46515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.1 4.17 72.9 0.737 0.928 0.555 0.526 2.2 1960
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 4.1 50 39147 2105 75.91 0.2447 0.2423 0.2892 0.2475 RANDOM 86.315
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] 6.86 -6.32 -2.18 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.881 r_dihedral_angle_3_deg 23.993 r_dihedral_angle_4_deg 20.3 r_dihedral_angle_1_deg 8.813 r_mcangle_it 6.528 r_mcbond_it 3.973 r_mcbond_other 3.973 r_angle_other_deg 3.673 r_angle_refined_deg 1.443 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.881 r_dihedral_angle_3_deg 23.993 r_dihedral_angle_4_deg 20.3 r_dihedral_angle_1_deg 8.813 r_mcangle_it 6.528 r_mcbond_it 3.973 r_mcbond_other 3.973 r_angle_other_deg 3.673 r_angle_refined_deg 1.443 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28132 Nucleic Acid Atoms 381 Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling