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OXA-24/40 in Complex with Boronic Acid BA3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 100 mM TRIS-HCl, pH 8.5, 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.15 70.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.083 α = 90 b = 103.083 β = 90 c = 86.437 γ = 90
Symmetry Space Group P 41 21 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 CCD RAYONIX MX-300 2015-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07807 APS 21-ID-D
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 2.28 103.08 99 0.099 15 7.9 21572
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 3PAE 2.28 103.08 20389 1060 98.62 0.20646 0.20419 0.2152 0.25202 0.2637 RANDOM 46.887
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] -4.16 -4.16 8.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.315 r_dihedral_angle_4_deg 20.844 r_dihedral_angle_3_deg 18.446 r_long_range_B_refined 8.763 r_dihedral_angle_1_deg 8.379 r_scbond_it 5.859 r_mcangle_it 5.346 r_mcbond_it 3.875 r_angle_refined_deg 2.237 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.315 r_dihedral_angle_4_deg 20.844 r_dihedral_angle_3_deg 18.446 r_long_range_B_refined 8.763 r_dihedral_angle_1_deg 8.379 r_scbond_it 5.859 r_mcangle_it 5.346 r_mcbond_it 3.875 r_angle_refined_deg 2.237 r_chiral_restr 0.178 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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_it r_scangle_other 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 1917 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing