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X-ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 at Room Temperature bound to tetraethylene glycol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9CXR Nyl50 structure solved at a slightly lowe resolution (2.2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.9 298 Imidazole 0.1 M pH 6.9, Polyethylene glycol 6,000 20.0% w/v
Crystal Properties Matthews coefficient Solvent content 2.18 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.879 α = 90 b = 96.511 β = 90 c = 105.188 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 2024-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.85 26.73 99.2 0.097 0.105 0.038 0.996 11.9 7.1 47261 22.6
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 1.85 1.89 90.7 0.662 0.751 0.34 0.703 4.3
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 FOURIER SYNTHESIS THROUGHOUT 1.85 26.73 44737 2470 99.13 0.1517 0.15057 0.1581 0.17219 0.1799 RANDOM 23.18
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] 0.1 0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.756 r_dihedral_angle_2_deg 9.452 r_long_range_B_refined 7.547 r_long_range_B_other 7.528 r_dihedral_angle_1_deg 6.555 r_scangle_other 6.245 r_scbond_it 4.103 r_scbond_other 4.103 r_mcangle_it 2.963 r_mcangle_other 2.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.756 r_dihedral_angle_2_deg 9.452 r_long_range_B_refined 7.547 r_long_range_B_other 7.528 r_dihedral_angle_1_deg 6.555 r_scangle_other 6.245 r_scbond_it 4.103 r_scbond_other 4.103 r_mcangle_it 2.963 r_mcangle_other 2.963 r_mcbond_it 2.111 r_mcbond_other 2.104 r_angle_refined_deg 1.735 r_angle_other_deg 0.591 r_chiral_restr 0.087 r_bond_refined_d 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4348 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction