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The 1.4 A structure of the class D beta-lactamase OXA-1 K70D complexed with oxacillin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6K PDB ENTRY 1M6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 10% (w/v) PEG 6000, 0.1 M NaCl, 0.05 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.14 42.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.919 α = 80.9 b = 72.609 β = 69.87 c = 73.446 γ = 71.44
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 MARMOSAIC 300 mm CCD 2012-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1 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 1.37 50 94.9 0.065 9.5 3.4 187539
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 1.37 1.42 91.6 0.421 3.2 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1M6K 1.37 33.23 187539 178142 9375 94.75 0.16476 0.16316 0.1724 0.19581 0.2007 RANDOM 21.186
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] 0.73 -0.01 0.28 0.86 0.07 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.055 r_dihedral_angle_4_deg 20.249 r_dihedral_angle_3_deg 13.903 r_dihedral_angle_1_deg 6.705 r_scbond_it 3.474 r_mcangle_it 2.821 r_mcbond_it 2.071 r_mcbond_other 2.07 r_angle_refined_deg 1.66 r_angle_other_deg 0.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.055 r_dihedral_angle_4_deg 20.249 r_dihedral_angle_3_deg 13.903 r_dihedral_angle_1_deg 6.705 r_scbond_it 3.474 r_mcangle_it 2.821 r_mcbond_it 2.071 r_mcbond_other 2.07 r_angle_refined_deg 1.66 r_angle_other_deg 0.838 r_chiral_restr 0.104 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it 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 7884 Nucleic Acid Atoms Solvent Atoms 945 Heterogen Atoms 171
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling