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Crystal structure of a class C beta-lactamase in complex with cefoxitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 0.1M sodium cacodylate pH 5.5
0.2M sodium chloride
35% polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.092 α = 90 b = 60.34 β = 111.93 c = 56.49 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2016-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.00 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.586 50 92.6 0.07 0.077 0.033 20.2 4.9 52020 10.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.62 95.7 0.213 0.243 0.115 0.96 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3IXH 1.59 41.21 1.53 51788 1995 92.62 0.16 0.1587 0.159 0.1913 0.1906 14.69
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 f_dihedral_angle_d 17.0371 f_angle_d 1.0628 f_chiral_restr 0.0657 f_bond_d 0.0085 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2718 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction Coot model building MOLREP phasing HKL-2000 data reduction