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Crystal structure of Nocardia cyriacigeorgica, class A beta-lactamase, NCY-1 bound to Avibactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M citric acid pH 6.5, 6 % ethylene glycol and 10 % Polyethylene Glycol 6000
Crystal Properties Matthews coefficient Solvent content 2.05 40.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.59 α = 90 b = 54.59 β = 90 c = 133.21 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M 2023-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999 SLS X06SA
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 1.3 44.55 100 0.064 0.999 16.62 10.6 57487 18.29
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 1.3 1.35 100 0.541 1.37 9.86
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.3 44.55 1.34 57484 2874 99.95 0.157 0.1561 0.1563 0.1752 0.1752 24.15
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 14.2021 f_angle_d 0.7938 f_chiral_restr 0.0652 f_plane_restr 0.0072 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1939 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing