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E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Old" crystal soaked with GTP, UTP, CTP, 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 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.358 α = 90 b = 153.766 β = 90 c = 231.686 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 5.4 49 99.4 0.996 6.68 6.2 16704
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 5.4 5.73 97.8 0.133 0.55 5
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 5.403 49 16495 770 98.167 0.298 0.2951 0.283 0.3625 0.3528 0 319.077
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] 0.335 0.565 -0.899
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 36.074 r_lrange_other 36.07 r_dihedral_angle_2_deg 28.411 r_dihedral_angle_3_deg 19.296 r_dihedral_angle_4_deg 17.14 r_mcangle_it 15.267 r_mcangle_other 15.267 r_scangle_it 11.581 r_scangle_other 11.557 r_mcbond_it 8.487
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 36.074 r_lrange_other 36.07 r_dihedral_angle_2_deg 28.411 r_dihedral_angle_3_deg 19.296 r_dihedral_angle_4_deg 17.14 r_mcangle_it 15.267 r_mcangle_other 15.267 r_scangle_it 11.581 r_scangle_other 11.557 r_mcbond_it 8.487 r_mcbond_other 8.486 r_dihedral_angle_1_deg 6.457 r_scbond_it 6.133 r_scbond_other 6.121 r_angle_refined_deg 1.347 r_symmetry_nbd_refined 0.619 r_nbd_other 0.504 r_symmetry_xyhbond_nbd_refined 0.462 r_angle_other_deg 0.458 r_xyhbond_nbd_refined 0.255 r_symmetry_nbd_other 0.225 r_nbd_refined 0.221 r_xyhbond_nbd_other 0.193 r_symmetry_xyhbond_nbd_other 0.166 r_nbtor_refined 0.154 r_ncsr_local_group_1 0.133 r_metal_ion_refined 0.116 r_chiral_restr 0.057 r_gen_planes_refined 0.054 r_gen_planes_other 0.049 r_bond_refined_d 0.005 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27578 Nucleic Acid Atoms 1459 Solvent Atoms Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing