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Crystal structure of yeast RNA polymerase II encountering 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 3.41 63.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.55 α = 90 b = 220.334 β = 97 c = 191.563 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 3.95 50 98.4 0.255 0.271 0.12 3.4 5.1 54937
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.95 4.02 97.7 0.937 0.455 0.779 4.7 2692
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.96 50 47410 2560 88.95 0.2513 0.2489 0.2427 0.2964 0.2905 RANDOM 147.355
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] 25.4 -13.07 -6.23 -15.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.9 r_dihedral_angle_3_deg 24.242 r_dihedral_angle_4_deg 19.886 r_mcangle_it 10.227 r_dihedral_angle_1_deg 9.224 r_mcbond_it 6.023 r_mcbond_other 6.023 r_angle_other_deg 3.67 r_angle_refined_deg 1.484 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.9 r_dihedral_angle_3_deg 24.242 r_dihedral_angle_4_deg 19.886 r_mcangle_it 10.227 r_dihedral_angle_1_deg 9.224 r_mcbond_it 6.023 r_mcbond_other 6.023 r_angle_other_deg 3.67 r_angle_refined_deg 1.484 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28121 Nucleic Acid Atoms 419 Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PHENIX refinement Coot model building