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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 6.5 289 PEG 4000, SODIUM CITRATE, MES, DTT
Crystal Properties Matthews coefficient Solvent content 5.53 77.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.79 α = 90 b = 393.36 β = 90 c = 281.6 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 2008-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 .979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 4 50 97.3 0.091 12.5 3.8 103153 103153 115.64
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 4 4.1 96.4 0.42 1.95 3.4
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 4 40 99551 2990 96.54 0.2103 0.2098 0.2323 0.2272 0.2501 RANDOM 196.34
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] 23.6113 39.4149 -63.0262
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.9 t_omega_torsion 2.41 t_angle_deg 1.13 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.9 t_omega_torsion 2.41 t_angle_deg 1.13 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 31693 Nucleic Acid Atoms 1795 Solvent Atoms Heterogen Atoms 11
Software Software Software Name Purpose BUSTER refinement SCALA data scaling PHASER phasing