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Structures of the transcriptional regulator BgaR, a lactose sensor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 5 mg/mL protein; 20% PEG 3350, 200 mM MgCl2. Sitting drops were 200 nL plus 200 nL at 20C- no buffer was used in this crystallisation cocktail.
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.15 α = 90 b = 46.317 β = 100.65 c = 118.903 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 EIGER X 16M 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.458650 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.87 48.25 99.5 0.087 0.037 0.998 9.4 6.6 87904
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 97.2 0.783 0.352 0.922 2.4 5.9
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 6nwh 1.87 46.86 83468 4408 99.39 0.22595 0.22449 0.235 0.25374 0.2591 RANDOM 28.33
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] 2.2 1.62 -1.03 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.268 r_dihedral_angle_4_deg 14.39 r_dihedral_angle_3_deg 13.216 r_long_range_B_refined 7.552 r_long_range_B_other 7.541 r_dihedral_angle_1_deg 6.455 r_scangle_other 5.424 r_scbond_it 3.496 r_scbond_other 3.496 r_mcangle_it 3.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.268 r_dihedral_angle_4_deg 14.39 r_dihedral_angle_3_deg 13.216 r_long_range_B_refined 7.552 r_long_range_B_other 7.541 r_dihedral_angle_1_deg 6.455 r_scangle_other 5.424 r_scbond_it 3.496 r_scbond_other 3.496 r_mcangle_it 3.375 r_mcangle_other 3.374 r_mcbond_it 2.349 r_mcbond_other 2.349 r_angle_refined_deg 1.47 r_angle_other_deg 1.364 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 7683 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing