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E. coli sigma-S transcription initiation complex with a 6-nt RNA and an NTP ("Old" crystal soaked with UTP, CTP, ddGTP, and dinucleotide ApG 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 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.936 α = 90 b = 153.772 β = 90 c = 232.616 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 2017-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 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 4.4 49.2 99.4 0.998 7.04 6.7 30874
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 4.4 4.66 97.3 0.208 0.43 6.7
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 4.4 49.148 30724 1464 99.199 0.347 0.3444 0.3335 0.3897 0.3742 0 280.214
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] 0.689 -0.215 -0.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.434 r_lrange_it 22.297 r_lrange_other 22.297 r_dihedral_angle_3_deg 19.38 r_dihedral_angle_4_deg 16.869 r_mcangle_it 8.47 r_mcangle_other 8.47 r_dihedral_angle_1_deg 6.565 r_scangle_it 6.194 r_scangle_other 6.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.434 r_lrange_it 22.297 r_lrange_other 22.297 r_dihedral_angle_3_deg 19.38 r_dihedral_angle_4_deg 16.869 r_mcangle_it 8.47 r_mcangle_other 8.47 r_dihedral_angle_1_deg 6.565 r_scangle_it 6.194 r_scangle_other 6.194 r_mcbond_it 4.698 r_mcbond_other 4.698 r_scbond_it 3.278 r_scbond_other 3.274 r_angle_refined_deg 1.399 r_angle_other_deg 0.714 r_symmetry_xyhbond_nbd_refined 0.343 r_xyhbond_nbd_refined 0.262 r_nbd_other 0.258 r_symmetry_nbd_other 0.231 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.215 r_symmetry_xyhbond_nbd_other 0.169 r_nbtor_refined 0.155 r_ncsr_local_group_1 0.127 r_chiral_restr 0.062 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 27530 Nucleic Acid Atoms 1349 Solvent Atoms Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing