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Crystal structure of leaf branch compost cutinase variant ICCG L50Y T110E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6THT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 10 mM Tris, 150 mM NaCl, 0.6 M succinic acid, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.19 61.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.21 α = 90 b = 97.21 β = 90 c = 74.67 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 6M 2024-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.000 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.64 48.605 98.5 0.999 15.98 26.18 1147084
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.74 0.517
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 1.64 48.605 43749 2188 98.596 0.204 0.2031 0.203 0.2277 0.2277 33.757
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] -0.855 -0.855 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.868 r_dihedral_angle_3_deg 11.33 r_dihedral_angle_2_deg 7.775 r_dihedral_angle_1_deg 6.978 r_lrange_it 6.257 r_scangle_it 4.736 r_scbond_it 3.716 r_mcangle_it 3.639 r_mcbond_it 2.992 r_angle_refined_deg 1.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.868 r_dihedral_angle_3_deg 11.33 r_dihedral_angle_2_deg 7.775 r_dihedral_angle_1_deg 6.978 r_lrange_it 6.257 r_scangle_it 4.736 r_scbond_it 3.716 r_mcangle_it 3.639 r_mcbond_it 2.992 r_angle_refined_deg 1.933 r_nbtor_refined 0.312 r_metal_ion_refined 0.29 r_nbd_refined 0.218 r_symmetry_nbd_refined 0.208 r_xyhbond_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.128 r_chiral_restr 0.124 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1945 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing