☰ Navigation Tabs
Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to cefotaxime
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 100 mM NaH2PO4, 100 mM citric acid, 200 mM NaCl, 20% PEG 8000, pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.095 α = 90 b = 143.032 β = 90 c = 44.312 γ = 90
Symmetry Space Group P 21 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 MARMOSAIC 300 mm CCD 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07814 APS 21-ID-D
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 1.81 98.1 99.9 0.084 0.046 0.998 13.1 7.8 57689
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 1.811 1.817 99.8 0.949 0.505 0.873 2.1 8.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4K0X 1.81 80.9 54798 2827 99.75 0.18115 0.17993 0.20458 0.241 RANDOM 41.969
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] 1.01 0.86 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.92 r_dihedral_angle_3_deg 12.447 r_dihedral_angle_4_deg 8.2 r_long_range_B_refined 8.198 r_long_range_B_other 8.197 r_scangle_other 5.852 r_dihedral_angle_1_deg 5.797 r_scbond_it 3.882 r_scbond_other 3.881 r_mcangle_other 3.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.92 r_dihedral_angle_3_deg 12.447 r_dihedral_angle_4_deg 8.2 r_long_range_B_refined 8.198 r_long_range_B_other 8.197 r_scangle_other 5.852 r_dihedral_angle_1_deg 5.797 r_scbond_it 3.882 r_scbond_other 3.881 r_mcangle_other 3.72 r_mcangle_it 3.716 r_mcbond_it 2.667 r_mcbond_other 2.659 r_angle_refined_deg 1.653 r_angle_other_deg 1.003 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3730 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing