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Crystal structure of Thermus thermophilus RNA polymerase holoenzyme in complex with GE23077
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DXJ PDB ENTRY 3DXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 295 A stock crystallization solution was prepared by adding T. thermophilus RNAP holoenzyme (10 mg/ml) in 20 mm TRIS-HCl, ph 7.7, 100 mm NaCl, and 1% glycerol to an equal volume of 33 mm magnesium formate containing 40 m ZnCl2. This solution was equilibrated against 35 mm magnesium formate and 30 mm sodium citrate, ph 5.4, vapor diffusion, hanging drop, temperature 295K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 4.75 74.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 236.569 α = 90 b = 236.569 β = 90 c = 252.311 γ = 120
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 270 2010-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91800 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.35 39.76 99.1 0.112 8.5428 5.81 113506 1.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.35 3.53 97.2 1 0.76 5.39
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3DXJ 3.35 38.971 1.35 113359 2265 98.9 0.2143 0.2138 0.2154 0.242 0.2406 156.78
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] 16.5497 16.5497 -33.0994
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.777 f_angle_d 0.846 f_chiral_restr 0.062 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26543 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing