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E. coli sigma-S transcription initiation complex with a 3-nt RNA and a mismatching ATP ("Fresh" crystal soaked with ATP for 2 hours)
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 2.71 54.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.096 α = 90 b = 154.918 β = 90 c = 231.775 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 2017-06-09 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 4.096 49.321 99.3 0.999 10.14 5 38147
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 4.096 4.34 97 0.108 5.06
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5IPL 4.096 49.3 37791 1809 98.304 0.325 0.3218 0.3103 0.3799 0.3658 304.517
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] 0.083 0.539 -0.621
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 34.406 r_lrange_other 34.406 r_dihedral_angle_2_deg 19.706 r_mcangle_it 17.64 r_mcangle_other 17.64 r_dihedral_angle_3_deg 15.938 r_scangle_it 14.169 r_scangle_other 14.169 r_dihedral_angle_4_deg 12.909 r_mcbond_it 10.252
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 34.406 r_lrange_other 34.406 r_dihedral_angle_2_deg 19.706 r_mcangle_it 17.64 r_mcangle_other 17.64 r_dihedral_angle_3_deg 15.938 r_scangle_it 14.169 r_scangle_other 14.169 r_dihedral_angle_4_deg 12.909 r_mcbond_it 10.252 r_mcbond_other 10.252 r_scbond_it 7.794 r_scbond_other 7.788 r_dihedral_angle_1_deg 5.433 r_angle_refined_deg 1.161 r_metal_ion_refined 0.681 r_symmetry_xyhbond_nbd_refined 0.481 r_angle_other_deg 0.459 r_nbd_other 0.344 r_symmetry_nbd_refined 0.296 r_xyhbond_nbd_other 0.258 r_xyhbond_nbd_refined 0.243 r_nbd_refined 0.211 r_symmetry_nbd_other 0.21 r_symmetry_xyhbond_nbd_other 0.195 r_nbtor_refined 0.162 r_ncsr_local_group_1 0.106 r_gen_planes_refined 0.052 r_gen_planes_other 0.047 r_chiral_restr 0.043 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27482 Nucleic Acid Atoms 1453 Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing