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Crystal structure of a leaf-branch compost cutinase variant (LCC_ICCG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7W45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M Sodium Nitrate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.081 α = 90 b = 88.081 β = 90 c = 73.738 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 EIGER X 16M 2024-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.7290 MAX IV BioMAX
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 1.64 47.626 99.5 0.108 0.112 0.03 0.999 17.2 25.9 35907
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 1.64 1.67 1.132 1.174 0.31 0.56 27
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 47.626 35866 1763 99.341 0.173 0.1706 0.1731 0.2117 0.2144 28.855
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] -0.036 -0.036 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.278 r_dihedral_angle_3_deg 11.646 r_dihedral_angle_2_deg 11.245 r_dihedral_angle_1_deg 6.964 r_lrange_other 6.395 r_lrange_it 6.378 r_scangle_it 5.304 r_scangle_other 5.302 r_scbond_it 3.775 r_scbond_other 3.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.278 r_dihedral_angle_3_deg 11.646 r_dihedral_angle_2_deg 11.245 r_dihedral_angle_1_deg 6.964 r_lrange_other 6.395 r_lrange_it 6.378 r_scangle_it 5.304 r_scangle_other 5.302 r_scbond_it 3.775 r_scbond_other 3.774 r_mcangle_other 3.416 r_mcangle_it 3.411 r_mcbond_it 2.682 r_mcbond_other 2.68 r_angle_refined_deg 1.797 r_angle_other_deg 0.64 r_symmetry_nbd_refined 0.63 r_nbd_other 0.256 r_nbd_refined 0.225 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.113 r_chiral_restr 0.095 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.01 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 1939 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing