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X-ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 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 BATCH MODE 293 Hampton Research PEGRx HT-D2 (Imidazole 0.1 M, Polyethylene glycol 6,000 20.0 w/v)
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.014 α = 90 b = 96.643 β = 90 c = 105.212 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 293 PIXEL DECTRIS EIGER R 4M Osmic VariMax 2024-03-26 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 2.2 25.38 98.63 0.1775 0.2012 0.093 0.94 9.98 4.4 28405 15.42
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 2.2 2.28 99.47 0.5051 0.5717 0.263 0.798
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 25.38 1.33 28317 1307 98.72 0.1605 0.1582 0.1592 0.2057 0.2067 18.16
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 15.4804 f_angle_d 0.4915 f_chiral_restr 0.042 f_plane_restr 0.0033 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4348 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing