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E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA 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 2.66 53.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.143 α = 90 b = 153.432 β = 90 c = 230.958 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 4.3 49 99.6 0.999 11.74 13.4 32436
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 4.3 4.56 98.6 0.22 0.54 13.1
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 4.305 48.975 32219 1541 98.974 0.307 0.3041 0.2992 0.3637 0.3548 0 308.26
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] -0.84 1.346 -0.506
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 30.074 r_lrange_other 30.057 r_dihedral_angle_2_deg 21.351 r_dihedral_angle_3_deg 15.974 r_dihedral_angle_4_deg 15.441 r_mcangle_it 14.393 r_mcangle_other 14.393 r_scangle_it 11.62 r_scangle_other 11.558 r_mcbond_it 8.22
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 30.074 r_lrange_other 30.057 r_dihedral_angle_2_deg 21.351 r_dihedral_angle_3_deg 15.974 r_dihedral_angle_4_deg 15.441 r_mcangle_it 14.393 r_mcangle_other 14.393 r_scangle_it 11.62 r_scangle_other 11.558 r_mcbond_it 8.22 r_mcbond_other 8.22 r_scbond_it 6.316 r_scbond_other 6.284 r_dihedral_angle_1_deg 6.123 r_angle_refined_deg 1.349 r_angle_other_deg 0.726 r_symmetry_xyhbond_nbd_refined 0.436 r_nbd_other 0.435 r_xyhbond_nbd_other 0.4 r_symmetry_nbd_refined 0.394 r_metal_ion_refined 0.354 r_symmetry_nbd_other 0.227 r_xyhbond_nbd_refined 0.225 r_nbd_refined 0.217 r_nbtor_refined 0.153 r_symmetry_xyhbond_nbd_other 0.152 r_ncsr_local_group_1 0.115 r_chiral_restr 0.056 r_gen_planes_refined 0.047 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 27482 Nucleic Acid Atoms 1441 Solvent Atoms Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing