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Crystal structure of MrtR bound to 3OH-C8 homoserine lactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 imidazole, MES, diethylene glycol, triethylene glycol, tetraethylene glycol, pentaethylene glycol, 2-Methyl-2,4-pentanediol (MPD), PEG 1000, PEG 3350, N-3-hydroxyoctanoyl-L-Homoserine lactone, DMSO. 2:1 protein:buffer
Crystal Properties Matthews coefficient Solvent content 2.34 47.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.315 α = 90 b = 35.552 β = 111.658 c = 61.649 γ = 90
Symmetry Space Group C 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 PILATUS 6M 2025-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 .980114 ESRF BM07
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.176 51 92.4 0.04 0.999 13.5 6.5 77750
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.176 1.197 96.4 0.385 6.3
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 (All) 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 1.176 51 77581 3872 92.129 0.147 0.1461 0.1529 0.1731 0.1753 RANDOM 21.406
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] -0.18 0.009 0.605 -0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.998 r_lrange_it 15.73 r_lrange_other 15.728 r_dihedral_angle_3_deg 11.354 r_scangle_it 10.207 r_scangle_other 10.204 r_mcangle_it 8.234 r_mcangle_other 8.234 r_scbond_it 7.421 r_scbond_other 7.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.998 r_lrange_it 15.73 r_lrange_other 15.728 r_dihedral_angle_3_deg 11.354 r_scangle_it 10.207 r_scangle_other 10.204 r_mcangle_it 8.234 r_mcangle_other 8.234 r_scbond_it 7.421 r_scbond_other 7.418 r_dihedral_angle_2_deg 6.611 r_mcbond_it 5.77 r_mcbond_other 5.746 r_dihedral_angle_1_deg 5.137 r_rigid_bond_restr 3.668 r_angle_refined_deg 1.659 r_angle_other_deg 0.619 r_nbd_refined 0.257 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.17 r_xyhbond_nbd_refined 0.158 r_nbd_other 0.152 r_symmetry_xyhbond_nbd_refined 0.118 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1918 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing