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Crystal structure of S. aureus BlaR1 sensor domain in complex with an imidazole 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 6 291 Sodium Cacodylate 0.085M pH 6.0 + PEG 8K 21% + Glycerol 15%
Crystal Properties Matthews coefficient Solvent content 2.38 48.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.027 α = 90 b = 107.943 β = 109.454 c = 56.39 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 2021-10-14 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 2 47.7 99.9 0.05 0.022 0.999 15.4 6.2 35815
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 2 2.05 100 1.758 0.767 0.589 1.1 6.2
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 2 47.698 35785 1797 99.891 0.19 0.1876 0.1952 0.2323 0.2373 58.404
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] -0.009 0.008 -0.011 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.345 r_dihedral_angle_3_deg 16.034 r_dihedral_angle_2_deg 10.611 r_lrange_it 9.394 r_lrange_other 9.393 r_scangle_other 7.142 r_scangle_it 6.985 r_dihedral_angle_1_deg 6.573 r_mcangle_it 5.901 r_mcangle_other 5.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.345 r_dihedral_angle_3_deg 16.034 r_dihedral_angle_2_deg 10.611 r_lrange_it 9.394 r_lrange_other 9.393 r_scangle_other 7.142 r_scangle_it 6.985 r_dihedral_angle_1_deg 6.573 r_mcangle_it 5.901 r_mcangle_other 5.9 r_scbond_it 4.746 r_scbond_other 4.745 r_mcbond_it 4.292 r_mcbond_other 4.283 r_angle_refined_deg 1.288 r_angle_other_deg 0.467 r_nbd_refined 0.207 r_symmetry_nbd_other 0.195 r_nbd_other 0.193 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.176 r_symmetry_nbd_refined 0.127 r_symmetry_xyhbond_nbd_refined 0.09 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_1 0.074 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4156 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing