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Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 Acylenzyme Complex at Room Temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model PDB 9DYS The authors state that both PDB entry 9DYS and an AF-model were used for re-phasing /-refining this model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.4 291 Imidazole 0.1 M pH 6.9, Polyethylene glycol 6,000 20.0% w/v
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.81 α = 90 b = 96.446 β = 90 c = 104.663 γ = 90
Symmetry Space Group P 2 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 298 PIXEL DECTRIS EIGER R 4M 2024-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541838
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.1 27.39 99.8 0.265 0.28 0.089 0.983 9.9 9.5 10389
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.31 100 0.587 0.619 0.195 0.903 9.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.1 27.39 1.34 19052 1897 99.86 0.1592 0.1534 0.1586 0.21 0.1614 RANDOM 9.54
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 17.2175 f_angle_d 1.2318 f_chiral_restr 0.0619 f_bond_d 0.0117 f_plane_restr 0.0114
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4298 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction