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E. coli sigma-S transcription initiation complex with an empty bubble ("Old" 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 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.069 α = 90 b = 153.3 β = 90 c = 230.897 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 2017-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
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 4.05 48.942 99.3 0.998 8.19 5.6 38603
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 4.05 4.29 97.1 0.181 0.56 5.65
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 4.05 48.9 38450 1841 98.889 0.283 0.2792 0.2739 0.3495 0.3346 247.661
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] 0.192 0.367 -0.559
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.455 r_lrange_other 24.454 r_dihedral_angle_2_deg 19.564 r_dihedral_angle_3_deg 16.086 r_dihedral_angle_4_deg 13.496 r_mcangle_it 12.227 r_mcangle_other 12.227 r_scangle_it 9.618 r_scangle_other 9.618 r_mcbond_it 7.067
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.455 r_lrange_other 24.454 r_dihedral_angle_2_deg 19.564 r_dihedral_angle_3_deg 16.086 r_dihedral_angle_4_deg 13.496 r_mcangle_it 12.227 r_mcangle_other 12.227 r_scangle_it 9.618 r_scangle_other 9.618 r_mcbond_it 7.067 r_mcbond_other 7.066 r_dihedral_angle_1_deg 5.74 r_scbond_it 5.241 r_scbond_other 5.241 r_angle_refined_deg 1.232 r_xyhbond_nbd_other 0.643 r_angle_other_deg 0.58 r_symmetry_xyhbond_nbd_refined 0.546 r_symmetry_nbd_refined 0.37 r_nbd_other 0.36 r_xyhbond_nbd_refined 0.233 r_symmetry_nbd_other 0.209 r_nbd_refined 0.208 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_other 0.151 r_ncsr_local_group_1 0.103 r_gen_planes_refined 0.049 r_chiral_restr 0.047 r_gen_planes_other 0.044 r_bond_refined_d 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27482 Nucleic Acid Atoms 1356 Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing