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E. coli sigma-S transcription initiation complex with a 4-nt RNA ("Fresh" crystal)
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 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.99 α = 90 b = 155.447 β = 90 c = 234.735 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 3.85 49.4 93.7 0.999 8.85 3.54 43708
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 3.85 4.09 90.2 0.193 0.49 3.25
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 3.854 49.396 43241 2059 92.643 0.271 0.2683 0.263 0.3293 0.3211 237.76
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] 0.2 0.307 -0.507
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 32.191 r_lrange_it 32.19 r_dihedral_angle_2_deg 22.44 r_mcangle_it 19.397 r_mcangle_other 19.397 r_scangle_other 16.907 r_scangle_it 16.906 r_dihedral_angle_3_deg 16.588 r_dihedral_angle_4_deg 16.432 r_mcbond_it 11.81
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 32.191 r_lrange_it 32.19 r_dihedral_angle_2_deg 22.44 r_mcangle_it 19.397 r_mcangle_other 19.397 r_scangle_other 16.907 r_scangle_it 16.906 r_dihedral_angle_3_deg 16.588 r_dihedral_angle_4_deg 16.432 r_mcbond_it 11.81 r_mcbond_other 11.807 r_scbond_it 9.905 r_scbond_other 9.903 r_dihedral_angle_1_deg 6.112 r_angle_refined_deg 1.389 r_symmetry_xyhbond_nbd_refined 0.47 r_angle_other_deg 0.464 r_xyhbond_nbd_other 0.439 r_nbd_other 0.369 r_symmetry_nbd_refined 0.361 r_xyhbond_nbd_refined 0.227 r_symmetry_nbd_other 0.223 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_other 0.179 r_nbtor_refined 0.153 r_ncsr_local_group_1 0.149 r_chiral_restr 0.054 r_gen_planes_refined 0.054 r_gen_planes_other 0.049 r_bond_refined_d 0.006 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27572 Nucleic Acid Atoms 1493 Solvent Atoms Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing