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Crystal structure of cutinase AdCut from Acidovorax delafieldii (PBS depolymerase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20 % PEG 3350,
0.2 M ammonium citrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.05 40.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.798 α = 90 b = 96.43 β = 111.033 c = 58.525 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 16M 2022-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.491 54.626 78.1 0.195 0.08 0.995 7.1 6.7 39403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.491 1.594 65.5 1.262 0.508 0.529 1.5 7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.491 54.626 39402 1897 51.098 0.177 0.1753 0.1851 0.2147 0.2218 10.792
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] 0.17 0.092 0.047 -0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.632 r_dihedral_angle_3_deg 12.922 r_dihedral_angle_2_deg 8.239 r_dihedral_angle_1_deg 7.082 r_lrange_it 3.854 r_lrange_other 3.722 r_scangle_it 1.743 r_scangle_other 1.742 r_angle_refined_deg 1.518 r_mcangle_other 1.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.632 r_dihedral_angle_3_deg 12.922 r_dihedral_angle_2_deg 8.239 r_dihedral_angle_1_deg 7.082 r_lrange_it 3.854 r_lrange_other 3.722 r_scangle_it 1.743 r_scangle_other 1.742 r_angle_refined_deg 1.518 r_mcangle_other 1.364 r_mcangle_it 1.36 r_scbond_it 1.109 r_scbond_other 1.105 r_mcbond_it 0.796 r_mcbond_other 0.792 r_angle_other_deg 0.549 r_xyhbond_nbd_refined 0.238 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.224 r_symmetry_nbd_refined 0.211 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.18 r_nbd_other 0.165 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.077 r_ncsr_local_group_1 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3976 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing