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Crystal structure of LmrR variant V15aY-RNYW with Val15 replaced by 3-aminotyrosine and evolved as Friedel-Crafts alkylase
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 8.5 294 The protein solution contained 16 mg/ml protein in 20 mM HEPES, pH 7, 280 mM NaCl. The reservoir solution contained 0.2 M Na-citrate, 0.1 M Bis-Tris propane, pH 8.5, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 24.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.7 α = 90 b = 58.533 β = 90 c = 74 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 2024-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 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 1.2 74 99.8 0.062 0.065 0.018 1 17.4 12.3 62694
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 1.2 1.22 96 2.211 2.36 0.803 0.409 8.1
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 1.2 45.95 59446 3173 99.77 0.17618 0.17425 0.1744 0.21268 0.213 RANDOM 20.756
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] -1.88 4.21 -2.33
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.376 r_dihedral_angle_3_deg 13.101 r_long_range_B_other 12.857 r_scangle_other 10.134 r_dihedral_angle_2_deg 7.213 r_scbond_it 7.062 r_scbond_other 7.036 r_mcangle_other 6.602 r_mcangle_it 6.593 r_rigid_bond_restr 6.078
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.376 r_dihedral_angle_3_deg 13.101 r_long_range_B_other 12.857 r_scangle_other 10.134 r_dihedral_angle_2_deg 7.213 r_scbond_it 7.062 r_scbond_other 7.036 r_mcangle_other 6.602 r_mcangle_it 6.593 r_rigid_bond_restr 6.078 r_dihedral_angle_1_deg 4.768 r_mcbond_it 4.532 r_mcbond_other 4.532 r_angle_refined_deg 1.721 r_angle_other_deg 0.617 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1831 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 12
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement