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Racemic crystal structures of Pribnow box consensus promoter sequence (Pnna)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Racemic DNA solution*, sodium cacodylate, magnesium chloride, sodium chloride, spermine tetrahydrochloride, MPD
*For crystallization, we used four strands
(1) d(CGCTATAATGCG) with L-sugars
(2) d(CGCATTATAGCG) with L-sugars
and
(3) d(CGCTATAATGCG) with D-sugars
(4) d(CGCATTATAGCG) with D-sugars
Enantio-pure L-DNA solution (strands 1,2) and D-DNA solution (strands 3,4) were prepared first with denaturation followed by slow annealing process to ensure proper folding of the duplex formed between the non-self complementary strands. After annealing, the enantiopure solutions were mixed in equimolar ratio and this racemic mixture was used for crystallization.
Crystal Properties Matthews coefficient Solvent content 2.32 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.905 α = 90 b = 68.454 β = 90 c = 34.211 γ = 90
Symmetry Space Group P n n a
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 PIXEL DECTRIS PILATUS 200K 2015-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 34.23 96.61 0.045 8.87 1.8 2825
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 2.3 2.38 78.57 0.175 1.34 1.6
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 1BNA 2.3 34.23 2678 147 96.58 0.27591 0.27162 0.2832 0.35745 0.3632 RANDOM 37.461
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] 2.18 -6.83 4.65
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.307 r_long_range_B_other 8.197 r_scangle_other 7.187 r_scbond_other 4.513 r_scbond_it 4.509 r_angle_refined_deg 1.668 r_angle_other_deg 1.6 r_chiral_restr 0.089 r_gen_planes_refined 0.019 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.307 r_long_range_B_other 8.197 r_scangle_other 7.187 r_scbond_other 4.513 r_scbond_it 4.509 r_angle_refined_deg 1.668 r_angle_other_deg 1.6 r_chiral_restr 0.089 r_gen_planes_refined 0.019 r_bond_refined_d 0.011 r_gen_planes_other 0.002 r_bond_other_d 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 486 Solvent Atoms 19 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing