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X-ray crystal structure of OXA-24/40 K84D in complex with cefotaxime
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M HEPES, 2% v/v PEG 4000, 2.0 M ammonium sulfate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.447 α = 90 b = 102.447 β = 90 c = 86.352 γ = 90
Symmetry Space Group P 41 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 RAYONIX MX-225 2012-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 1.62 50 98.6 0.097 8.4 7.7 58160
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 1.62 1.68 97.2 0.76 6.1
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 3PAE 1.62 27.76 54994 2928 98.44 0.1795 0.1785 0.1994 0.2173 RANDOM 27.339
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] -1.44 -1.44 2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.728 r_dihedral_angle_4_deg 20.058 r_dihedral_angle_3_deg 14.719 r_dihedral_angle_1_deg 5.855 r_angle_refined_deg 2.005 r_angle_other_deg 1.548 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.728 r_dihedral_angle_4_deg 20.058 r_dihedral_angle_3_deg 14.719 r_dihedral_angle_1_deg 5.855 r_angle_refined_deg 2.005 r_angle_other_deg 1.548 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1928 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction