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Crystal structure of a cutinase enzyme from Thermobifida fusca NTU22 (702)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZOA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 20 % PEG 3350,
0.2 M sodium sulfate,
0.1 M Bis-Tris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.346 α = 86.28 b = 79.753 β = 87.94 c = 120.133 γ = 89.5
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 2021-01-27 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 1.637 119.804 89.5 0.09 0.055 0.998 9 3.6 140392
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 1.637 1.748 53.6 0.772 0.481 0.567 1.5 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5zoa 1.64 119.8 133556 6780 76.62 0.1668 0.1652 0.1751 0.1991 0.2076 RANDOM 20.544
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] 0.12 -0.05 0.03 0.06 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.19 r_dihedral_angle_4_deg 18.874 r_dihedral_angle_3_deg 10.925 r_dihedral_angle_1_deg 6.762 r_angle_refined_deg 1.632 r_angle_other_deg 1.483 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.19 r_dihedral_angle_4_deg 18.874 r_dihedral_angle_3_deg 10.925 r_dihedral_angle_1_deg 6.762 r_angle_refined_deg 1.632 r_angle_other_deg 1.483 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11924 Nucleic Acid Atoms Solvent Atoms 1515 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction STARANISO data scaling MOLREP phasing