☰ Navigation Tabs
ToxR bacterial transcriptional regulator bound to 20 bp toxT promoter DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GXP PhoB DNA binding domain (1GXP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% PEG 4000, 0.1 M sodium acetate pH 4, 0.15 M
ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.5 α = 90 b = 54.209 β = 92.58 c = 63.657 γ = 90
Symmetry Space Group P 1 21 1
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 2013-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
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 2.07 63.59 99.82 0.105 16.32 7.8 14625
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 2.07 2.14 1.016
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PhoB DNA binding domain (1GXP) 2.07 63.59 14625 734 99.77 0.18494 0.1823 0.24107 0.2337 RANDOM 36.446
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] -0.82 -0.68 -2.29 3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.079 r_dihedral_angle_4_deg 21.186 r_dihedral_angle_3_deg 13.839 r_long_range_B_refined 7.882 r_long_range_B_other 7.843 r_dihedral_angle_1_deg 6.809 r_scangle_other 5.826 r_scbond_it 3.938 r_scbond_other 3.936 r_mcangle_it 3.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.079 r_dihedral_angle_4_deg 21.186 r_dihedral_angle_3_deg 13.839 r_long_range_B_refined 7.882 r_long_range_B_other 7.843 r_dihedral_angle_1_deg 6.809 r_scangle_other 5.826 r_scbond_it 3.938 r_scbond_other 3.936 r_mcangle_it 3.553 r_mcangle_other 3.549 r_mcbond_it 2.535 r_mcbond_other 2.526 r_angle_refined_deg 1.729 r_angle_other_deg 1.226 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 886 Nucleic Acid Atoms 814 Solvent Atoms 177 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing