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Crystal structure of the multidrug binding transcriptional regulator LmrR in complex squaraine dye
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 100 mM Hepes, pH 7.5, 5 mM NiCl2, 5 mM MgCl2, 5 mM CdCl2, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.56 51.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.658 α = 90 b = 68.019 β = 90 c = 200.858 γ = 90
Symmetry Space Group P 21 21 21
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 2019-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.48459 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.6 100.429 100 0.144 0.159 0.047 9.4 11.5 19703 19703
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 100 2.667 2.667 2.863 0.834 0.2 11.6
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 3f8b 2.6 64.51 18650 990 99.96 0.2445 0.2407 0.2454 0.3167 0.3123 RANDOM 84.846
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] -2.92 3.72 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.625 r_dihedral_angle_3_deg 23.661 r_dihedral_angle_4_deg 16.434 r_dihedral_angle_1_deg 7.413 r_angle_refined_deg 1.819 r_angle_other_deg 1.268 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.625 r_dihedral_angle_3_deg 23.661 r_dihedral_angle_4_deg 16.434 r_dihedral_angle_1_deg 7.413 r_angle_refined_deg 1.819 r_angle_other_deg 1.268 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3174 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction