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E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Fresh" crystal soaked with CTP, GTP, and ddTTP 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 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.854 α = 90 b = 154.252 β = 90 c = 230.729 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 2017-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 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 4.097 49.2 98.6 0.999 9.94 6.1 37445
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 4.097 4.34 94.2 0.097 0.5 6.2
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 4.097 49.176 37248 1774 98.042 0.335 0.3322 0.3195 0.3955 0.3786 0 265.99
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] -0.593 0.326 0.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.635 r_lrange_it 28.451 r_lrange_other 28.45 r_dihedral_angle_3_deg 19.413 r_dihedral_angle_4_deg 17.333 r_mcangle_it 13.826 r_mcangle_other 13.826 r_scangle_it 11.474 r_scangle_other 11.473 r_mcbond_it 7.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.635 r_lrange_it 28.451 r_lrange_other 28.45 r_dihedral_angle_3_deg 19.413 r_dihedral_angle_4_deg 17.333 r_mcangle_it 13.826 r_mcangle_other 13.826 r_scangle_it 11.474 r_scangle_other 11.473 r_mcbond_it 7.99 r_mcbond_other 7.99 r_dihedral_angle_1_deg 6.693 r_scbond_it 6.347 r_scbond_other 6.339 r_angle_refined_deg 1.453 r_angle_other_deg 0.907 r_metal_ion_refined 0.527 r_symmetry_xyhbond_nbd_refined 0.523 r_xyhbond_nbd_other 0.429 r_nbd_other 0.365 r_symmetry_nbd_refined 0.341 r_xyhbond_nbd_refined 0.267 r_symmetry_nbd_other 0.241 r_nbd_refined 0.232 r_symmetry_xyhbond_nbd_other 0.199 r_nbtor_refined 0.157 r_ncsr_local_group_1 0.134 r_chiral_restr 0.065 r_gen_planes_refined 0.042 r_gen_planes_other 0.038 r_bond_refined_d 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27578 Nucleic Acid Atoms 1434 Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing