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Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the no-metal bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6U0Y PDBID 6U0Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.2 M sodium malonate pH 7.0, 20 % w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.467 α = 90 b = 104.467 β = 90 c = 99.035 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 100 PIXEL DECTRIS PILATUS3 X 6M 2019-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97911 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 50 98.7 0.119 31 14.6 29676 35.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 83.2 0.898 0.552 0.67 6.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDBID 6U0Y 1.8 41.15 0.31 29445 1511 97.88 0.1927 0.191 0.1898 0.2243 0.2262 random 45.63
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 13.7707 f_angle_d 0.7748 f_chiral_restr 0.0512 f_plane_restr 0.0057 f_bond_d 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2003 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing