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E. coli sigma-S transcription initiation complex with 3-nt RNA ("Old" crystal soaked with GTP and ATP 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 295 PEG3350, sodium chloride, HEPES
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.468 α = 90 b = 153.228 β = 90 c = 229.171 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 4.4 49.7 98.6 0.999 8.01 6.6 29564
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 4.67 92.2 0.11 0.51 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 4.404 49.7 29033 1380 96.78 0.3 0.2966 0.2866 0.3629 0.3503 0 299.369
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] 0.791 -0.637 -0.154
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 40.875 r_lrange_other 40.874 r_dihedral_angle_2_deg 21.165 r_mcangle_it 21.104 r_mcangle_other 21.104 r_scangle_it 17.221 r_scangle_other 17.213 r_dihedral_angle_3_deg 16.107 r_dihedral_angle_4_deg 14.398 r_mcbond_it 12.183
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 40.875 r_lrange_other 40.874 r_dihedral_angle_2_deg 21.165 r_mcangle_it 21.104 r_mcangle_other 21.104 r_scangle_it 17.221 r_scangle_other 17.213 r_dihedral_angle_3_deg 16.107 r_dihedral_angle_4_deg 14.398 r_mcbond_it 12.183 r_mcbond_other 12.183 r_scbond_it 9.479 r_scbond_other 9.476 r_dihedral_angle_1_deg 5.701 r_angle_refined_deg 1.149 r_metal_ion_refined 0.565 r_angle_other_deg 0.424 r_nbd_other 0.317 r_symmetry_nbd_refined 0.284 r_xyhbond_nbd_refined 0.233 r_nbd_refined 0.224 r_symmetry_nbd_other 0.22 r_symmetry_xyhbond_nbd_refined 0.215 r_symmetry_xyhbond_nbd_other 0.196 r_nbtor_refined 0.147 r_ncsr_local_group_1 0.104 r_gen_planes_refined 0.052 r_gen_planes_other 0.047 r_chiral_restr 0.044 r_bond_other_d 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27482 Nucleic Acid Atoms 1431 Solvent Atoms Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing