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Crystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12 at Room Temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 0.09 M HEPES, pH 6.8, 27% w/v PEG3350, 5% v/v cholin acetate (HR Ionic Liquid 5), protein:cocktail ratio of 2:1
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.593 α = 90 b = 79.428 β = 90 c = 108.777 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 Osmic VariMax 2025-04-01 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 1.9 29.64 99.9 0.063 0.069 0.028 0.989 13.3 5.9 53622
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 1.9 1.94 99.9 0.637 0.737 0.364 0.723 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 29.37 50888 2688 99.8 0.15327 0.15104 0.1625 0.19585 0.2007 RANDOM 31.37
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] 0.35 -0.66 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.499 r_dihedral_angle_2_deg 14.264 r_long_range_B_refined 9.462 r_long_range_B_other 9.462 r_scangle_other 8.98 r_dihedral_angle_1_deg 6.904 r_scbond_it 6.342 r_scbond_other 6.341 r_mcangle_other 5.129 r_mcangle_it 5.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.499 r_dihedral_angle_2_deg 14.264 r_long_range_B_refined 9.462 r_long_range_B_other 9.462 r_scangle_other 8.98 r_dihedral_angle_1_deg 6.904 r_scbond_it 6.342 r_scbond_other 6.341 r_mcangle_other 5.129 r_mcangle_it 5.127 r_mcbond_it 3.97 r_mcbond_other 3.969 r_angle_refined_deg 2.293 r_angle_other_deg 0.811 r_chiral_restr 0.139 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4657 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction