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Crystal structure of metagenomic class A beta-lactamase precursor LRA-5 in complex with ceftazidime at 2.35 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E25 1E25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 294 1.6 M sodium formate
Crystal Properties Matthews coefficient Solvent content 3.41 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.08 α = 90 b = 162.11 β = 90 c = 70.27 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 9M convex prefocusing mirror and a Kirkpatrick-Baez pair of focusing mirrors 2021-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.35 43.66 99.7 0.283 0.997 11.78 13.4 36200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.49 98.1 2.33 0.495 1.62 12.72
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 THROUGHOUT 1E25 2.35 43.66 1.33 36122 1806 99.92 0.1968 0.1958 0.1955 0.216 0.2157 46
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 8.217 f_angle_d 1.036 f_chiral_restr 0.05 f_plane_restr 0.016 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4016 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction Aimless data scaling PHENIX phasing Coot model building