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Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl10 at Cryo 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 BATCH MODE 4.7 293 0.5 M DL-malic acid pH 4.7, 15% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.13 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.126 α = 90 b = 120.193 β = 92.99 c = 148.305 γ = 90
Symmetry Space Group C 1 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 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 1.3 74.05 98.8 0.044 0.059 0.039 0.999 10.7 3.9 351281
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 1.32 99.2 0.985 1.316 0.865 0.44 1.4 3.8
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 1.3 68.4 333519 17757 98.8 0.14387 0.14247 0.1427 0.17013 0.1704 RANDOM 23.399
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] 2.89 1.03 -0.28 -2.7
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.551 r_long_range_B_other 13.887 r_dihedral_angle_2_deg 12.532 r_dihedral_angle_3_deg 11.185 r_scangle_other 11.159 r_mcangle_it 8.278 r_mcangle_other 8.267 r_scbond_it 8.237 r_scbond_other 8.236 r_dihedral_angle_1_deg 6.68
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.551 r_long_range_B_other 13.887 r_dihedral_angle_2_deg 12.532 r_dihedral_angle_3_deg 11.185 r_scangle_other 11.159 r_mcangle_it 8.278 r_mcangle_other 8.267 r_scbond_it 8.237 r_scbond_other 8.236 r_dihedral_angle_1_deg 6.68 r_mcbond_it 6.243 r_mcbond_other 6.214 r_rigid_bond_restr 5.199 r_angle_refined_deg 1.694 r_angle_other_deg 0.622 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11558 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling autoPROC data processing PHASER phasing CrysalisPro data reduction