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Crystal structure of S. aureus BlaR1 sensor domain in complex with a boronate inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.25 291 Sodium Cacodylate 0.085M pH 5.25 + PEG 8K 21% + Glycerol 15%
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.904 α = 90 b = 106.78 β = 108.092 c = 56.278 γ = 90
Symmetry Space Group P 1 21 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 2022-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.97 47.83 98.7 0.077 0.035 0.998 10.6 5.3 36626
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.02 99 1.578 0.747 0.534 1.1 5.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.97 47.829 36599 1814 98.398 0.197 0.195 0.2034 0.2367 0.2384 47.161
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] -0.031 -0.183 0.021 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.014 r_dihedral_angle_3_deg 14.011 r_dihedral_angle_2_deg 7.588 r_dihedral_angle_1_deg 6.679 r_lrange_it 5.886 r_lrange_other 5.882 r_scangle_it 3.928 r_scangle_other 3.927 r_mcangle_it 3.435 r_mcangle_other 3.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.014 r_dihedral_angle_3_deg 14.011 r_dihedral_angle_2_deg 7.588 r_dihedral_angle_1_deg 6.679 r_lrange_it 5.886 r_lrange_other 5.882 r_scangle_it 3.928 r_scangle_other 3.927 r_mcangle_it 3.435 r_mcangle_other 3.434 r_scbond_it 2.48 r_scbond_other 2.478 r_mcbond_it 2.215 r_mcbond_other 2.213 r_angle_refined_deg 1.073 r_angle_other_deg 0.438 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.205 r_symmetry_nbd_other 0.19 r_nbd_other 0.19 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.054 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4214 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing