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Crystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12 at Cryo Temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9Z0A same protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 7.4 291 0.09 M HEPES, pH 6.8, 27% w/v PEG3350, 5% v/v cholin acetate (HR Ionic Liquid 5), protein:ML ratio of 2:1
Crystal Properties Matthews coefficient Solvent content 2.06 40.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.623 α = 90 b = 135.407 β = 90 c = 142.882 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 EIGER X 16M 2025-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979460 SSRL BL12-1
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 1.75 98.28 93.7 0.134 0.145 0.055 0.992 8.2 6.8 217968
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 1.75 1.78 98 1.177 1.28 0.497 0.646 6.4
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 1.75 98.28 207043 10809 93.57 0.16293 0.16117 0.1707 0.19653 0.2044 RANDOM 22.645
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] -1.04 -0.04 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.149 r_dihedral_angle_2_deg 13.223 r_long_range_B_other 7.827 r_long_range_B_refined 7.826 r_scangle_other 7.409 r_dihedral_angle_1_deg 6.857 r_scbond_it 5.247 r_scbond_other 5.237 r_mcangle_other 3.943 r_mcangle_it 3.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.149 r_dihedral_angle_2_deg 13.223 r_long_range_B_other 7.827 r_long_range_B_refined 7.826 r_scangle_other 7.409 r_dihedral_angle_1_deg 6.857 r_scbond_it 5.247 r_scbond_other 5.237 r_mcangle_other 3.943 r_mcangle_it 3.942 r_mcbond_it 3.05 r_mcbond_other 3.043 r_angle_refined_deg 2.225 r_angle_other_deg 0.89 r_chiral_restr 0.181 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 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 18743 Nucleic Acid Atoms Solvent Atoms 831 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction autoPROC data reduction