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Crystal structure of LmrR variant V15aY with Val15 replaced by 3-aminotyrosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 The protein solution contained 16 mg/ml protein in 20 mM HEPES, 280 mM NaCl, pH 7.0. The reservoir solution contained 0.2 M KSCN, 0.1 M Bis-Tris propane, pH 6.5, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.87 57.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.714 α = 90 b = 70.714 β = 90 c = 59.838 γ = 120
Symmetry Space Group P 32 1 2
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 2.15 61.26 100 0.05 0.053 0.016 1 17.4 10.2 9471
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 2.15 2.21 100 1.854 1.951 0.603 0.705 10.3
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 (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 2.15 42.84 8993 474 99.95 0.22357 0.22122 0.2335 0.26819 0.2791 RANDOM 75.912
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] -1.21 -0.6 -1.21 3.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.536 r_long_range_B_refined 12.821 r_long_range_B_other 12.819 r_scangle_other 9.14 r_dihedral_angle_2_deg 8.619 r_mcangle_other 7.791 r_mcangle_it 7.781 r_scbond_it 6.502 r_scbond_other 6.497 r_dihedral_angle_1_deg 6.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.536 r_long_range_B_refined 12.821 r_long_range_B_other 12.819 r_scangle_other 9.14 r_dihedral_angle_2_deg 8.619 r_mcangle_other 7.791 r_mcangle_it 7.781 r_scbond_it 6.502 r_scbond_other 6.497 r_dihedral_angle_1_deg 6.294 r_mcbond_it 5.796 r_mcbond_other 5.76 r_angle_refined_deg 1.985 r_angle_other_deg 0.697 r_chiral_restr 0.102 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 928 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing