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Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O5I PDB ENTRY 2O5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 30% MPD, 0.1M NA CACODYLATE, 0.2M MG ACETATE, 2MM AMPCPP, 2MM STD, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 6.50, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.85 68.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.379 α = 90 b = 155.379 β = 90 c = 496.992 γ = 90
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 MARMOSAIC 300 mm CCD 2006-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 40 88.7 0.11 0.11 7.1 2.6 207148 207148 47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 70.1 0.439 0.439 2.2 1.9 16469
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2O5I 3 40 207148 207148 11916 87.8 0.243 0.234 0.234 0.234 0.266 0.2599 RANDOM 55.1
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 c_dihedral_angle_d 26.8 c_angle_deg 1.84 c_improper_angle_d 1.37 c_bond_d 0.016 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.8 c_angle_deg 1.84 c_improper_angle_d 1.37 c_bond_d 0.016 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47168 Nucleic Acid Atoms 2168 Solvent Atoms 2470 Heterogen Atoms 156
Software Software Software Name Purpose AMoRE phasing CNS refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling