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Beta-lactamase mixed with Ceftriaxone, 5ms
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 MICROBATCH 300 Ammonium Phosphate
Crystal Properties Matthews coefficient Solvent content 3.76 67.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.68 α = 90 b = 98.78 β = 108.6 c = 113.09 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 2.4 25 100 0.99 6.67 1758 65232
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 2.4 2.44 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 2.40005625978 24.695 52163 2550 79.2582125384 0.235226856236 0.234404553417 0.2355 0.25040738568 0.2505 45.1175667829
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 12.9681413205 f_angle_d 1.06948363718 f_chiral_restr 0.0485709695414 f_plane_restr 0.00444590974272 f_bond_d 0.00335102753402
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7952 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement CrystFEL data scaling PDB_EXTRACT data extraction CrystFEL data reduction MOLREP phasing