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CRYSTAL STRUCTURE OF R220A VARIANT PENA BETA-LACTAMASE FROM BURKHOLDERIA MULTIVORANS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 250microL reservoir (25% polyethylene glycol 8kDa (PEG 8000), 0.1 M MES at pH 6.5)), 4microL hanging drop (7.5 mg/ml protein, 12.5% PEG 8000, 0.05M MES at pH 6.5). Adding Acetone to the drop (final 4%) improved the crystal size and shape.
Crystal Properties Matthews coefficient Solvent content 1.95 36.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.343 α = 90 b = 71.158 β = 90.045 c = 84.541 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 2018-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 1.51 42.27 99.6 0.056 0.064 0.056 12.5 3.8 114986 13.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.53 92.5 0.365 0.427 0.218 2.5 3.7
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 3W4Q 1.51 42.27 1.19 113415 5670 98.21 0.1747 0.1737 0.1737 0.1928 0.1919 16.37
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 13.5656 f_angle_d 0.8291 f_chiral_restr 0.0491 f_plane_restr 0.0053 f_bond_d 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5730 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing