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Crystal structure of the ligand-binding domain of a putative GntR-family transcriptional regulator from Bordetella bronchiseptica
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 273 0.1M Bis-tris pH 7.0, 1M Tri-ammonium citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.77 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.196 α = 82.36 b = 58.071 β = 86.52 c = 65.58 γ = 68.31
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 APS-1 Mirrors 2008-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97934 APS 19-BM
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 50 97.6 0.122 0.122 18.387 4.1 52604 52604 -3 34
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 2.03 95.8 0.382 0.382 3 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2 29.91 51591 51591 2614 0.167 0.167 0.164 0.3049 0.217 0.0601 RANDOM 16.59
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] 1.2 0.56 -0.84 -1.91 0.53 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.955 r_dihedral_angle_4_deg 18.243 r_dihedral_angle_3_deg 14.767 r_dihedral_angle_1_deg 7.012 r_scangle_it 5.404 r_scbond_it 3.367 r_mcangle_it 2.102 r_angle_refined_deg 1.922 r_angle_other_deg 1.44 r_mcbond_it 1.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.955 r_dihedral_angle_4_deg 18.243 r_dihedral_angle_3_deg 14.767 r_dihedral_angle_1_deg 7.012 r_scangle_it 5.404 r_scbond_it 3.367 r_mcangle_it 2.102 r_angle_refined_deg 1.922 r_angle_other_deg 1.44 r_mcbond_it 1.162 r_mcbond_other 0.339 r_chiral_restr 0.113 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4999 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 57
Software Software Software Name Purpose HKL-3000 data collection HKL-2000 data reduction HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-2000 data scaling DM phasing