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E. coli sigma-S transcription initiation complex with a 4-nt RNA and a UTP ("Old" crystal soaked with UTP, ddCTP, 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 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.395 α = 90 b = 154.105 β = 90 c = 232.152 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 0.97918 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 4.2 49.1 99.1 0.999 7.53 6.8 35121
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 4.2 4.45 95.2 0.114 0.46 6.8
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 4.201 49.077 34963 1678 98.872 0.345 0.3425 0.3304 0.389 0.3738 0 251.227
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] 0.154 -0.06 -0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.681 r_lrange_it 23.899 r_lrange_other 23.899 r_dihedral_angle_3_deg 19.54 r_dihedral_angle_4_deg 17.193 r_mcangle_it 10.399 r_mcangle_other 10.398 r_scangle_it 8.089 r_scangle_other 8.089 r_dihedral_angle_1_deg 6.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.681 r_lrange_it 23.899 r_lrange_other 23.899 r_dihedral_angle_3_deg 19.54 r_dihedral_angle_4_deg 17.193 r_mcangle_it 10.399 r_mcangle_other 10.398 r_scangle_it 8.089 r_scangle_other 8.089 r_dihedral_angle_1_deg 6.714 r_mcbond_it 5.841 r_mcbond_other 5.841 r_scbond_it 4.35 r_scbond_other 4.35 r_angle_refined_deg 1.45 r_angle_other_deg 1.017 r_nbd_other 0.401 r_symmetry_xyhbond_nbd_refined 0.386 r_symmetry_nbd_refined 0.35 r_xyhbond_nbd_refined 0.268 r_symmetry_nbd_other 0.239 r_nbd_refined 0.228 r_metal_ion_refined 0.206 r_symmetry_xyhbond_nbd_other 0.16 r_nbtor_refined 0.157 r_ncsr_local_group_1 0.133 r_chiral_restr 0.067 r_gen_planes_refined 0.038 r_gen_planes_other 0.035 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27579 Nucleic Acid Atoms 1396 Solvent Atoms Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing