Navigation Tabs Crystal Structure of the Metallo Beta Lactamase L1 from Stenotrophomonas maltophilia Determined by Serial Crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UA1 PDBID 6UA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 289 Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350.
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.668 α = 90 b = 105.668 β = 90 c = 99.332 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 297 PIXEL DECTRIS PILATUS3 X 6M 2019-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Nylon Mesh fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 60um Nylon mesh ALEX mesh-holder SmarAct XYZ stage PMAC EPICS
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 7186 7186
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (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 1.85 46.66 99.99 0.942 0.197 4.08 57.37 28773 6.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 0.818 0.362 1.15 29.22
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 PDBID 6UA1 1.85 46.65 1.41 28496 1441 99.99 0.1773 0.1752 0.17 0.2167 0.22 13.42
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 17.0366 f_angle_d 0.7614 f_chiral_restr 0.05 f_bond_d 0.0057 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1988 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement REFMAC refinement MOLREP phasing cctbx.prime data scaling DIALS data reduction
