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Crystal structure of S. aureus BlaR1 sensor domain in complex with cefepime
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XA7 BlaR1 sensor domain apo structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.25 291 Soidum Cacodylate 0.085M pH 5.5 + PEG 8K 27% + Glycerol 15%
Crystal Properties Matthews coefficient Solvent content 2.11 41.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.819 α = 90 b = 109.47 β = 103.657 c = 50.297 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 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.0064 ALBA XALOC
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 2.153 45.537 82.55 0.13 0.142 0.057 0.9969 9.186 6.05 17584
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 2.153 2.345 1.772 0.865 0.3028
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 2.52 45.537 15112 778 90.605 0.219 0.2165 0.2143 0.27 0.2636 54.16
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] -0.294 3.124 3.39 -4.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.567 r_dihedral_angle_6_deg 13.85 r_dihedral_angle_1_deg 6.113 r_lrange_it 3.507 r_lrange_other 3.483 r_dihedral_angle_2_deg 3.438 r_mcangle_it 2.012 r_mcangle_other 2.012 r_scangle_it 1.679 r_scangle_other 1.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.567 r_dihedral_angle_6_deg 13.85 r_dihedral_angle_1_deg 6.113 r_lrange_it 3.507 r_lrange_other 3.483 r_dihedral_angle_2_deg 3.438 r_mcangle_it 2.012 r_mcangle_other 2.012 r_scangle_it 1.679 r_scangle_other 1.679 r_mcbond_it 1.113 r_mcbond_other 1.113 r_angle_refined_deg 0.917 r_scbond_it 0.91 r_scbond_other 0.91 r_angle_other_deg 0.338 r_nbd_other 0.237 r_symmetry_xyhbond_nbd_refined 0.202 r_nbd_refined 0.192 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.165 r_symmetry_nbd_refined 0.129 r_ncsr_local_group_1 0.08 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.076 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4140 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing