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E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP and UTP 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 2.74 55.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.933 α = 90 b = 155.987 β = 90 c = 233.576 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 3.8 49.4 99.5 0.999 9.01 6.7 48197
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 3.8 4.03 98.5 0.169 0.46 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 3.803 49.4 47895 2301 98.883 0.277 0.2737 0.27 0.3433 0.3341 0 236.335
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] 0.737 -0.701 -0.037
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 25.612 r_lrange_it 25.611 r_dihedral_angle_2_deg 22.453 r_dihedral_angle_3_deg 16.738 r_dihedral_angle_4_deg 15.238 r_mcangle_it 14.093 r_mcangle_other 14.093 r_scangle_it 11.737 r_scangle_other 11.735 r_mcbond_it 8.416
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 25.612 r_lrange_it 25.611 r_dihedral_angle_2_deg 22.453 r_dihedral_angle_3_deg 16.738 r_dihedral_angle_4_deg 15.238 r_mcangle_it 14.093 r_mcangle_other 14.093 r_scangle_it 11.737 r_scangle_other 11.735 r_mcbond_it 8.416 r_mcbond_other 8.416 r_scbond_it 6.651 r_scbond_other 6.648 r_dihedral_angle_1_deg 6.542 r_angle_refined_deg 1.349 r_symmetry_xyhbond_nbd_refined 0.466 r_angle_other_deg 0.454 r_symmetry_nbd_refined 0.352 r_nbd_other 0.335 r_xyhbond_nbd_other 0.243 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.213 r_nbd_refined 0.204 r_ncsr_local_group_1 0.163 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.155 r_chiral_restr 0.053 r_gen_planes_refined 0.053 r_gen_planes_other 0.048 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