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The crystal structure of a beta-lactamase from Shigella flexneri 2a str. 2457T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.1M HEPES:NaOH
30% (w/v) PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.419 α = 90 b = 73.767 β = 92.397 c = 109.512 γ = 90
Symmetry Space Group P 1 21 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 2020-03-03 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 1.8 46.4 98.2 0.116 0.134 0.067 0.988 19.1 3.8 66678 -3 18.81
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 1.8 1.83 86.5 0.559 0.68 0.377 0.661 2.4 2.8
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 6DPZ 1.8 46.38 1.36 66647 3315 97.77 0.1546 0.1527 0.1531 0.1916 0.1912 23.86
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 14.482 f_angle_d 0.8556 f_chiral_restr 0.0565 f_bond_d 0.0068 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5569 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 138
Software Software Software Name Purpose SBC-Collect data collection PHENIX refinement HKL-3000 phasing HKL-3000 data reduction HKL-3000 data scaling