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Crystal structure of OXA-46 beta-lactamase from P. aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1M Na,K L-tartrate tetrahydrate, 50mM Hepes, 2-4%(v/v) PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.838 α = 90 b = 123.838 β = 90 c = 327.915 γ = 120
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 MAR CCD 165 mm 2005-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.92 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 56.5 98.7 0.065 0.065 9.6 8.8 48568 48227 1.2 42.418
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 98.7 0.61 0.61 1.2 7.78 756
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3HBR 2.4 31.4 2 34100 34100 3404 100 0.21793 0.21793 0.21115 0.2112 0.28519 0.2845 RANDOM 40.818
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.879 r_dihedral_angle_3_deg 19.65 r_dihedral_angle_4_deg 18.803 r_dihedral_angle_1_deg 7.355 r_scangle_it 3.051 r_scbond_it 1.995 r_angle_refined_deg 1.607 r_mcangle_it 1.422 r_mcbond_it 0.81 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.879 r_dihedral_angle_3_deg 19.65 r_dihedral_angle_4_deg 18.803 r_dihedral_angle_1_deg 7.355 r_scangle_it 3.051 r_scbond_it 1.995 r_angle_refined_deg 1.607 r_mcangle_it 1.422 r_mcbond_it 0.81 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.293 r_symmetry_hbond_refined 0.29 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5825 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 63
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling