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E. coli mutant sigma-S transcription initiation complex with an 8-nt RNA ("Fresh" mutant crystal soaked with GTP, UTP, CTP, and ddATP for 30 minutes)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 PEG3350, sodium chloride, HEPES
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.184 α = 90 b = 153.474 β = 90 c = 230.825 γ = 90
Symmetry Space Group P 21 21 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-F 2017-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97910 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 5.395 49 99 0.995 6.93 5.9 16580
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 5.4 5.72 95.4 0.157 0.47 5.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5IPL 5.4 48.988 16477 771 98.323 0.317 0.3142 0.3051 0.3622 0.3508 0 279.166
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] -0.093 0.844 -0.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.506 r_lrange_it 27.793 r_lrange_other 27.786 r_dihedral_angle_3_deg 19.424 r_dihedral_angle_4_deg 16.444 r_mcangle_it 10.054 r_mcangle_other 10.053 r_scangle_it 7.073 r_scangle_other 7.022 r_dihedral_angle_1_deg 6.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.506 r_lrange_it 27.793 r_lrange_other 27.786 r_dihedral_angle_3_deg 19.424 r_dihedral_angle_4_deg 16.444 r_mcangle_it 10.054 r_mcangle_other 10.053 r_scangle_it 7.073 r_scangle_other 7.022 r_dihedral_angle_1_deg 6.546 r_mcbond_it 5.505 r_mcbond_other 5.505 r_scbond_it 3.665 r_scbond_other 3.639 r_angle_refined_deg 1.383 r_angle_other_deg 0.715 r_symmetry_xyhbond_nbd_refined 0.347 r_nbd_other 0.346 r_symmetry_nbd_refined 0.325 r_xyhbond_nbd_refined 0.262 r_symmetry_nbd_other 0.232 r_xyhbond_nbd_other 0.225 r_nbd_refined 0.222 r_symmetry_xyhbond_nbd_other 0.219 r_nbtor_refined 0.155 r_ncsr_local_group_1 0.131 r_metal_ion_refined 0.113 r_chiral_restr 0.061 r_gen_planes_refined 0.048 r_gen_planes_other 0.043 r_bond_refined_d 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27525 Nucleic Acid Atoms 1407 Solvent Atoms Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing