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L2 class A serine-beta-lactamase in complex with cyclic boronate 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 Crystal reagent (1.5 uL): 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M DL-Glutamic acid; 0.02 M DL-Alanine; 0.02 M Glycine; 0.02 M DL-Lysine; 0.02 M DL-Serine, 0.1 M bicine/Trizma base pH 8.5
Protein (1 uL): 42 mg/ml, 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM imidazole, 1 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.9 57.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.38 α = 90 b = 85.69 β = 90 c = 113.18 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M-F 2016-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.09 44.1 99.3 0.126 0.992 8 13.1 40861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.14 99.5 0.8 0.534 1.4 13.3
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 5NE2 2.09 42.845 1.34 40861 2034 99.13 0.1776 0.1756 0.1792 0.2143 0.216
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 14.33 f_angle_d 1.249 f_chiral_restr 0.059 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4018 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing