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Crystal Structure of an Engineered OXA-10 Variant with Carbapenemase Activity, OXA-10loop24
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K55 PDB ENTRY 1K55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 2.8 M ammonium sulfate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.65 53.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.33 α = 90 b = 81.33 β = 90 c = 151.921 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 MARMOSAIC 225 mm CCD 2009-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 1.95 33.43 99.9 0.086 9.2 3.2 85904 81931 17.7
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 1.95 2.06 100 0.323 3.3 3.1 11977
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 PDB ENTRY 1K55 1.95 25.82 77737 77737 4100 99.95 0.16852 0.16852 0.16636 0.1669 0.20967 0.2073 RANDOM 23.631
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.652 r_dihedral_angle_4_deg 18.996 r_dihedral_angle_3_deg 14.658 r_dihedral_angle_1_deg 5.531 r_scangle_it 4.516 r_scbond_it 2.797 r_mcangle_it 1.872 r_angle_refined_deg 1.616 r_mcbond_it 1.033 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.652 r_dihedral_angle_4_deg 18.996 r_dihedral_angle_3_deg 14.658 r_dihedral_angle_1_deg 5.531 r_scangle_it 4.516 r_scbond_it 2.797 r_mcangle_it 1.872 r_angle_refined_deg 1.616 r_mcbond_it 1.033 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 7690 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 127
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling