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The crystal structure of a beta lactamase from Xanthomonas campestris pv. campestris str. ATCC 33913
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.2 M sodium chloride
0.1 M Tris:HCl
1.0 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.262 α = 90 b = 66.894 β = 112.656 c = 43.895 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 PIXEL DECTRIS PILATUS3 S 6M 2020-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.5 45 97.4 0.102 0.114 0.05 0.989 32.3 5.1 40433 -3 17.45
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 1.5 1.53 80.9 0.483 0.565 0.282 0.788 2.25 3
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 5X5G 1.5 44.88 1.38 40408 2004 97.13 0.1608 0.1595 0.1597 0.186 0.1865 25.43
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 20.5407 f_angle_d 1.0241 f_chiral_restr 0.0873 f_bond_d 0.0086 f_plane_restr 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2014 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement SBC-Collect data collection HKL-3000 phasing HKL-3000 data reduction HKL-3000 data scaling