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Crystal Structure of a Rationally Designed OXA-10 Variant Showing Carbapenemase Activity, OXA-10loop48
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K55 PCD ENTRY 1K55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 298 2.9 M ammonium sulfate, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.21 α = 90 b = 97.01 β = 90 c = 125.87 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 ADSC QUANTUM 4r Diamond(111), Ge(220) 2008-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.6 28.76 98.2 0.069 15.8 7 79252 79252 17.5
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 1.6 1.68 95.8 0.372 4.4 6.5 11124
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 (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 PCD ENTRY 1K55 1.6 24.83 75189 75189 3983 98.06 0.1749 0.1749 0.17351 0.1726 0.20138 0.2002 RANDOM 21.55
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.928 r_dihedral_angle_4_deg 15.098 r_dihedral_angle_3_deg 11.954 r_dihedral_angle_1_deg 5.183 r_scangle_it 3.699 r_scbond_it 2.219 r_mcangle_it 1.402 r_angle_refined_deg 1.342 r_mcbond_it 0.742 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.928 r_dihedral_angle_4_deg 15.098 r_dihedral_angle_3_deg 11.954 r_dihedral_angle_1_deg 5.183 r_scangle_it 3.699 r_scbond_it 2.219 r_mcangle_it 1.402 r_angle_refined_deg 1.342 r_mcbond_it 0.742 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3869 Nucleic Acid Atoms Solvent Atoms 543 Heterogen Atoms 80
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling