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Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 PEG 6000, Ammonium Acetate, Sodium Acetate, DTT
Crystal Properties Matthews coefficient Solvent content 5.53 77.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.05 α = 90 b = 390.94 β = 90 c = 278.08 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.4 195.47 89.3 0.319 0.373 0.189 3.2 3.5 145314 145314 59.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.58 55.4 1.413 1.413 0.854 0.5 3.2 13052
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 3FKI 3.7 40 122114 3691 96.43 0.2012 0.2006 0.2334 0.2197 0.2562 RANDOM 134.22
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] 9.3655 12.4017 -21.7672
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.66 t_omega_torsion 2 t_angle_deg 1.09 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.66 t_omega_torsion 2 t_angle_deg 1.09 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31475 Nucleic Acid Atoms 1033 Solvent Atoms Heterogen Atoms 11
Software Software Software Name Purpose BUSTER-TNT refinement SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing