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Crystal Structure of OXA-45, a Class D beta-lactamase with extended spectrum activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5
22% PEG 4K
10% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.169 α = 90 b = 47.488 β = 90 c = 108.903 γ = 90
Symmetry Space Group P 21 21 21
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 BRUKER SMART 6000 2005-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.01 30 100 0.141 5.4 16275
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 2.01 2.08 99.9 0.435 1591
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 1M6K 2.01 27.226 16228 818 99.93 0.1685 0.166 0.1669 0.2161 0.2164 RANDOM 18.1965
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] 0.83 -0.37 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.663 r_sphericity_free 23.879 r_dihedral_angle_4_deg 19.721 r_dihedral_angle_3_deg 12.537 r_sphericity_bonded 5.831 r_dihedral_angle_1_deg 5.598 r_rigid_bond_restr 2.674 r_angle_refined_deg 1.121 r_chiral_restr 0.074 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.663 r_sphericity_free 23.879 r_dihedral_angle_4_deg 19.721 r_dihedral_angle_3_deg 12.537 r_sphericity_bonded 5.831 r_dihedral_angle_1_deg 5.598 r_rigid_bond_restr 2.674 r_angle_refined_deg 1.121 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1831 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction