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Structure of the OXA-1 class D beta-lactamase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FOF PDB entries 1FOF and 1E4D experimental model PDB 1E4D PDB entries 1FOF and 1E4D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG 8000 (10/20%), 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.02 α = 70.19 b = 51.62 β = 84.11 c = 72.89 γ = 81.51
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 4 1999-02-13 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 2001-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.935 CHESS A1 2 SYNCHROTRON CHESS BEAMLINE A1 0.929 CHESS A1
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 1.49 50 86.5 0.049 0.049 23.6 2.6 69837 69837 -3 12.8
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) 1.5 1.55 36.9 0.123 0.123 5.9 1.5 2979
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 entries 1FOF and 1E4D 1.5 48.21 68784 68784 1396 88.1 0.182 0.182 0.182 0.1823 0.203 0.2016 RANDOM 16.4
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 c_dihedral_angle_d 22.1 c_scangle_it 2.644 c_scbond_it 1.808 c_mcangle_it 1.574 c_angle_deg 1.41 c_mcbond_it 1.039 c_improper_angle_d 0.81 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3931 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling EPMR phasing CNS refinement