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E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP, UTP, GTP, and ddATP for 150 seconds)
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 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.532 α = 90 b = 155.431 β = 90 c = 232.601 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 2017-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
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 3.45 49.3 99.7 0.999 12.95 12.3 63761
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 3.45 3.66 98.4 0.216 0.52 12.24
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5IPL 3.45 49.279 63485 3029 99.24 0.285 0.2819 0.2769 0.348 0.3389 180.678
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] 0.118 0.094 -0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.542 r_lrange_it 17.105 r_lrange_other 17.105 r_dihedral_angle_3_deg 15.306 r_dihedral_angle_4_deg 13.532 r_mcangle_it 9.116 r_mcangle_other 9.116 r_scangle_it 7.735 r_scangle_other 7.728 r_dihedral_angle_1_deg 5.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.542 r_lrange_it 17.105 r_lrange_other 17.105 r_dihedral_angle_3_deg 15.306 r_dihedral_angle_4_deg 13.532 r_mcangle_it 9.116 r_mcangle_other 9.116 r_scangle_it 7.735 r_scangle_other 7.728 r_dihedral_angle_1_deg 5.973 r_mcbond_it 5.434 r_mcbond_other 5.434 r_scbond_it 4.461 r_scbond_other 4.455 r_angle_refined_deg 1.341 r_angle_other_deg 0.441 r_symmetry_xyhbond_nbd_refined 0.355 r_symmetry_nbd_refined 0.308 r_nbd_other 0.285 r_symmetry_nbd_other 0.21 r_xyhbond_nbd_refined 0.203 r_nbd_refined 0.196 r_ncsr_local_group_1 0.175 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.138 r_gen_planes_refined 0.054 r_chiral_restr 0.05 r_gen_planes_other 0.049 r_bond_refined_d 0.006 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27579 Nucleic Acid Atoms 1471 Solvent Atoms Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing