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Crystal structure of MrtR bound to 7Z-3OH-C14 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 7.4 277 magnesium chloride, calcium chloride, sodium HEPES, MOPS, ethylene glycol, PEG 8000, N-(3-hydroxy-7-cis-tetradecenoyl)-L-homoserine lactone
Crystal Properties Matthews coefficient Solvent content 3 59.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.1 α = 90 b = 120.793 β = 98.58 c = 122.601 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 EIGER X 16M 2025-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979338 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.06 42.8 93.2 0.954 4 6.07 17089
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 3.06 3.111 100 0.35
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 MOLECULAR REPLACEMENT THROUGHOUT 3.06 42.8 16275 804 93.1 0.25799 0.25625 0.256 0.29424 0.297 RANDOM 62.303
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] -0.56 2.35 -0.5 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.036 r_dihedral_angle_2_deg 6.095 r_dihedral_angle_1_deg 3.73 r_long_range_B_refined 2.905 r_long_range_B_other 2.905 r_mcangle_it 1.408 r_mcangle_other 1.408 r_scangle_other 0.933 r_angle_refined_deg 0.842 r_mcbond_it 0.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.036 r_dihedral_angle_2_deg 6.095 r_dihedral_angle_1_deg 3.73 r_long_range_B_refined 2.905 r_long_range_B_other 2.905 r_mcangle_it 1.408 r_mcangle_other 1.408 r_scangle_other 0.933 r_angle_refined_deg 0.842 r_mcbond_it 0.757 r_mcbond_other 0.757 r_scbond_it 0.458 r_scbond_other 0.458 r_angle_other_deg 0.326 r_chiral_restr 0.035 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5577 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing