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Crystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA operator site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P5K N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS) experimental model PDB 1JFS N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.1 277 1.7M ammonium sulphate, 0.1M HEPES, 0.1M sodium chloride, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.10
Crystal Properties Matthews coefficient Solvent content 4.77 74.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.105 α = 90 b = 118.77 β = 90 c = 121.23 γ = 90
Symmetry Space Group I 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 CCD ADSC QUANTUM 4 MIRRORS 2003-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 2.85 24.81 98 0.063 0.063 18 4.1 23191 75.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 98 0.406 0.406 3.4 4.1
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 N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS) 2.85 24.81 23191 1198 97.5 0.208 0.207 0.196 0.231 0.2155 RANDOM 23.9
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] -0.89 0.53 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.998 r_dihedral_angle_4_deg 23.381 r_dihedral_angle_3_deg 18.637 r_dihedral_angle_1_deg 5.263 r_angle_refined_deg 1.675 r_mcangle_it 1.173 r_scangle_it 0.874 r_mcbond_it 0.695 r_scbond_it 0.587 r_nbtor_refined 0.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.998 r_dihedral_angle_4_deg 23.381 r_dihedral_angle_3_deg 18.637 r_dihedral_angle_1_deg 5.263 r_angle_refined_deg 1.675 r_mcangle_it 1.173 r_scangle_it 0.874 r_mcbond_it 0.695 r_scbond_it 0.587 r_nbtor_refined 0.346 r_symmetry_vdw_refined 0.344 r_nbd_refined 0.251 r_symmetry_hbond_refined 0.246 r_xyhbond_nbd_refined 0.211 r_chiral_restr 0.069 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms 1448 Solvent Atoms 13 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing