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Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XDM PDB ENTRY 2XDM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 pH 6
Crystal Properties Matthews coefficient Solvent content 2.58 52.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.88 α = 90 b = 91.353 β = 94.27 c = 106.919 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 CCD MARRESEARCH SX-165 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 46 99.8 0.1 15.1 99.8 69063
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.56 2.9 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2XDM 2.5 42 65546 3493 99.8 0.19772 0.19464 0.1918 0.25384 0.2494 RANDOM 39.546
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] 0.05 -0.1 0.13 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.238 r_dihedral_angle_3_deg 17.429 r_dihedral_angle_4_deg 15.961 r_dihedral_angle_1_deg 6.384 r_scangle_it 2.695 r_scbond_it 1.67 r_angle_refined_deg 1.455 r_mcangle_it 1.031 r_mcbond_it 0.548 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.238 r_dihedral_angle_3_deg 17.429 r_dihedral_angle_4_deg 15.961 r_dihedral_angle_1_deg 6.384 r_scangle_it 2.695 r_scbond_it 1.67 r_angle_refined_deg 1.455 r_mcangle_it 1.031 r_mcbond_it 0.548 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13394 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling