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Crystal structure of leaf branch compost cutinase variant ICCG L50Y Q183K
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 2.95 58.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.57 α = 90 b = 96.57 β = 90 c = 73.16 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 1.71 48.29 99.5 0.806 19.09 25.93 964320
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 1.71 1.81 97 0.806 1.06
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 1.71 48.285 37807 1891 99.636 0.173 0.1713 0.1713 0.2038 0.2039 30.692
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] -0.408 -0.408 0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.711 r_dihedral_angle_3_deg 11.123 r_dihedral_angle_2_deg 8.164 r_lrange_it 7.096 r_dihedral_angle_1_deg 7.013 r_scangle_it 4.984 r_scbond_it 3.938 r_mcangle_it 3.302 r_mcbond_it 2.671 r_angle_refined_deg 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.711 r_dihedral_angle_3_deg 11.123 r_dihedral_angle_2_deg 8.164 r_lrange_it 7.096 r_dihedral_angle_1_deg 7.013 r_scangle_it 4.984 r_scbond_it 3.938 r_mcangle_it 3.302 r_mcbond_it 2.671 r_angle_refined_deg 1.98 r_symmetry_nbd_refined 0.369 r_symmetry_xyhbond_nbd_refined 0.355 r_nbtor_refined 0.316 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.215 r_chiral_restr 0.135 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1943 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing