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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 5.7 293 5 mg/mL protein; 21.7% PEG 3350, 222mM MgCl2, 100mM bis-tris pH 5.7. Sitting drops were set up in 200 nL plus 200 nL volumes at 20C
Crystal Properties Matthews coefficient Solvent content 2.13 42.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.429 α = 90 b = 40.482 β = 90.33 c = 261.721 γ = 90
Symmetry Space Group I 1 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 DECTRIS EIGER X 16M 2018-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953723 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 2.11 43.62 98.7 0.103 0.043 0.997 9.4 6.7 41261
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 2.11 2.17 91.7 0.672 0.29 0.744 2.7 6.3
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 2.11 43.6 39182 2066 98.59 0.19559 0.19376 0.2011 0.2305 0.2338 RANDOM 40.041
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] -1.1 -0.21 2.97 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.48 r_dihedral_angle_4_deg 15.453 r_dihedral_angle_3_deg 14.253 r_long_range_B_refined 9.176 r_long_range_B_other 9.175 r_scangle_other 6.704 r_dihedral_angle_1_deg 6.49 r_mcangle_it 4.532 r_mcangle_other 4.532 r_scbond_it 4.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.48 r_dihedral_angle_4_deg 15.453 r_dihedral_angle_3_deg 14.253 r_long_range_B_refined 9.176 r_long_range_B_other 9.175 r_scangle_other 6.704 r_dihedral_angle_1_deg 6.49 r_mcangle_it 4.532 r_mcangle_other 4.532 r_scbond_it 4.356 r_scbond_other 4.356 r_mcbond_it 3.216 r_mcbond_other 3.21 r_angle_refined_deg 1.427 r_angle_other_deg 1.334 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 5036 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing