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Beta-lactamase mixed with Ceftriaxone, 50ms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 300 Ammonium Phosphate
Crystal Properties Matthews coefficient Solvent content 3.77 67.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.41 α = 90 b = 98.16 β = 109.76 c = 115.16 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 300 PIXEL AGIPD 2020-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE SPB/SFX 1.33 European XFEL SPB/SFX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 24.9 100 0.97 5.5 749 50760
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.65 0.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 6B5X 2.60006254355 24.8287331207 45264 2218 87.1937124364 0.225263796382 0.222726700129 0.2225 0.275011204447 0.2729 35.3141550322
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 13.4497390812 f_angle_d 1.34322008761 f_chiral_restr 0.0556171119586 f_plane_restr 0.00404312465635 f_bond_d 0.00309391066903
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7952 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 164
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction CrystFEL data reduction PHASER phasing