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E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Old" crystal soaked with GTP, ATP, CTP, and ddTTP 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 53.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.555 α = 90 b = 153.578 β = 90 c = 231.214 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 49.1 99.3 0.999 10.59 6.8 40237
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 4.24 96.4 0.171 0.48 6.5
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 4.002 49.08 40013 1924 98.685 0.307 0.3032 0.2979 0.3804 0.3707 0 276.41
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] 0.768 0.226 -0.994
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 29.783 r_lrange_other 29.783 r_dihedral_angle_2_deg 28.662 r_dihedral_angle_3_deg 19.561 r_dihedral_angle_4_deg 17.641 r_mcangle_it 16.557 r_mcangle_other 16.557 r_scangle_it 13.295 r_scangle_other 13.294 r_mcbond_it 9.785
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 29.783 r_lrange_other 29.783 r_dihedral_angle_2_deg 28.662 r_dihedral_angle_3_deg 19.561 r_dihedral_angle_4_deg 17.641 r_mcangle_it 16.557 r_mcangle_other 16.557 r_scangle_it 13.295 r_scangle_other 13.294 r_mcbond_it 9.785 r_mcbond_other 9.785 r_scbond_it 7.44 r_scbond_other 7.433 r_dihedral_angle_1_deg 6.575 r_angle_refined_deg 1.399 r_metal_ion_refined 0.716 r_angle_other_deg 0.549 r_symmetry_xyhbond_nbd_refined 0.434 r_xyhbond_nbd_other 0.359 r_nbd_other 0.324 r_symmetry_nbd_refined 0.302 r_xyhbond_nbd_refined 0.254 r_symmetry_nbd_other 0.233 r_nbd_refined 0.226 r_nbtor_refined 0.156 r_symmetry_xyhbond_nbd_other 0.15 r_ncsr_local_group_1 0.132 r_chiral_restr 0.059 r_gen_planes_refined 0.052 r_gen_planes_other 0.047 r_bond_refined_d 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27578 Nucleic Acid Atoms 1434 Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing