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Crystal structure of LmrR with V15 replaced by unnatural amino acid 4-mercaptophenylalanine, Au(I) bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 Sitting drops prepared with protein solution (0.412 mM protein, 0.824 mM KAuCN2, 20 mM MOPS, pH 7.0, 150 mM NaCl) and reservoir crystallization solution (0.2 M NaF, 0.1 M Bis-Tris propane, pH 7.5, 20% PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.44 α = 90 b = 52.715 β = 90 c = 146.194 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 2023-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 48.73 100 0.12 0.127 0.041 0.998 11.1 9.4 10107
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 1.34 1.427 0.482 0.726 8.6
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 2.5 42.79 9540 521 99.96 0.24783 0.24514 0.2547 0.29397 0.2984 RANDOM 74.172
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] -5.75 10.21 -4.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.807 r_long_range_B_refined 15.336 r_long_range_B_other 15.336 r_scangle_other 12.083 r_mcangle_it 9.754 r_mcangle_other 9.75 r_dihedral_angle_2_deg 8.07 r_scbond_it 7.506 r_scbond_other 7.502 r_mcbond_it 6.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.807 r_long_range_B_refined 15.336 r_long_range_B_other 15.336 r_scangle_other 12.083 r_mcangle_it 9.754 r_mcangle_other 9.75 r_dihedral_angle_2_deg 8.07 r_scbond_it 7.506 r_scbond_other 7.502 r_mcbond_it 6.551 r_mcbond_other 6.519 r_dihedral_angle_1_deg 6.124 r_angle_refined_deg 1.817 r_angle_other_deg 0.679 r_chiral_restr 0.351 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 1824 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement