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Crystal structures of Pribnow box consensus promoter sequence (P32)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 463D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 MPD, sodium cacodylate, zinc chloride, spermine
Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.906 α = 90 b = 46.906 β = 90 c = 99.044 γ = 120
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 200K 2016-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.81 40.62 99.3 0.0283 0.0369 17.08 1.98 5955
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.81 2.91 96.5 0.1357 3.87 1.91
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 463D 2.81 40.62 5584 319 98.86 0.22707 0.22587 0.2269 0.24801 0.2436 RANDOM 41.455
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] 14.21 14.21 -28.43
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 10.263 r_long_range_B_other 10.216 r_scangle_other 5.592 r_scbond_other 4.042 r_scbond_it 4.04 r_angle_refined_deg 1.787 r_angle_other_deg 1.748 r_chiral_restr 0.086 r_gen_planes_refined 0.013 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 10.263 r_long_range_B_other 10.216 r_scangle_other 5.592 r_scbond_other 4.042 r_scbond_it 4.04 r_angle_refined_deg 1.787 r_angle_other_deg 1.748 r_chiral_restr 0.086 r_gen_planes_refined 0.013 r_bond_refined_d 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1362 Solvent Atoms 72 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing