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Crystal structure of the organohalide sensing RdhR-CbdbA1625 transcriptional regulator in the ligand free form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Crystals formed in 0.1M Tris pH 7.5, 0.3M sodium acetate, 15% w/v PEG 4K were flash-cooled in liquid nitrogen by supplementing the mother liquor with 10% PEG 200.
Crystal Properties Matthews coefficient Solvent content 3.12 60.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.95 α = 90 b = 71.95 β = 90 c = 87.63 γ = 120
Symmetry Space Group P 31 2 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 PSI PILATUS 6M 2011-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.987 Diamond I04
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 1.392 31.16 99.78 0.048 19.4 6.7 50241 50241
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 1.392 1.428 96.4 0.566 3 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.392 31.16 50241 2688 99.78 0.13721 0.1355 0.1354 0.16929 0.1692 RANDOM 19.195
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] 0.03 0.02 0.03 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.436 r_sphericity_free 28.426 r_sphericity_bonded 17.424 r_dihedral_angle_4_deg 15.899 r_dihedral_angle_3_deg 13.392 r_rigid_bond_restr 9.428 r_scbond_it 5.688 r_long_range_B_refined 5.463 r_dihedral_angle_1_deg 4.857 r_mcbond_it 3.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.436 r_sphericity_free 28.426 r_sphericity_bonded 17.424 r_dihedral_angle_4_deg 15.899 r_dihedral_angle_3_deg 13.392 r_rigid_bond_restr 9.428 r_scbond_it 5.688 r_long_range_B_refined 5.463 r_dihedral_angle_1_deg 4.857 r_mcbond_it 3.126 r_mcangle_it 2.975 r_angle_refined_deg 2.348 r_chiral_restr 0.158 r_bond_refined_d 0.026 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1374 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MLPHARE phasing