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Crystal Structure of Oxa-10 Beta-Lactamase Covalently Bound to Cyclobutanone Beta-Lactam Mimic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E4D PDB entry 1e4d
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 1.4 M sodium potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.7 α = 90 b = 82.544 β = 94.63 c = 102.36 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2008-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.917 102.062 97.3 0.082 0.082 13.9 3.4 84571 84571
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) 2 2.12 99.3 0.35 0.35 2.2 3.4 11881
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 REFMAC rigid body refinement THROUGHOUT PDB entry 1e4d 2 102.06 73266 3651 99.36 0.181 0.178 0.233 0.202 RANDOM 20.045
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] 0.24 -0.48 -0.12 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.482 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_1_deg 5.663 r_scangle_it 4.903 r_scbond_it 3.025 r_angle_refined_deg 1.78 r_mcangle_it 1.738 r_mcbond_it 0.99 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.482 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_1_deg 5.663 r_scangle_it 4.903 r_scbond_it 3.025 r_angle_refined_deg 1.78 r_mcangle_it 1.738 r_mcbond_it 0.99 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7862 Nucleic Acid Atoms Solvent Atoms 917 Heterogen Atoms 106
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection REFMAC phasing