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Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 in its Apo form at Room Temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9DYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.4 291 1.8 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 6.9
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.755 α = 90 b = 96.398 β = 90 c = 104.618 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 2024-10-22 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 30.72 98 0.199 0.207 0.056 0.994 11.8 13.2 27717
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 2.27 97.3 0.786 0.82 0.226 0.731 13.1
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 2.2 28.27 26208 1462 97.65 0.15047 0.1479 0.15 0.19645 0.1896 RANDOM 19.223
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] 0.14 0.68 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.172 r_dihedral_angle_2_deg 12.787 r_long_range_B_refined 10.17 r_long_range_B_other 10.163 r_scangle_other 8.075 r_dihedral_angle_1_deg 6.945 r_scbond_it 5.546 r_scbond_other 5.545 r_mcangle_it 3.901 r_mcangle_other 3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.172 r_dihedral_angle_2_deg 12.787 r_long_range_B_refined 10.17 r_long_range_B_other 10.163 r_scangle_other 8.075 r_dihedral_angle_1_deg 6.945 r_scbond_it 5.546 r_scbond_other 5.545 r_mcangle_it 3.901 r_mcangle_other 3.9 r_mcbond_it 2.775 r_mcbond_other 2.772 r_angle_refined_deg 2.046 r_angle_other_deg 0.673 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 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 172 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction