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Crystal structure of fungal cutinase from Aspergillus fumigatiaffinis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 25% PEG3350, 0.1 M HEPES pH7.5
Crystal Properties Matthews coefficient Solvent content 1.96 37.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.053 α = 90 b = 63.053 β = 90 c = 215.316 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2022-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.8 50 96.4 0.107 0.119 0.051 0.984 8.9 4.5 4184
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 2.8 2.85 95.8 0.307 0.369 0.2 0.703 2.7
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 4OHY 2.8 33.84 3985 199 96.38 0.17735 0.1723 0.1791 0.27537 0.2588 RANDOM 49.066
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] -0.62 -0.31 -0.62 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.034 r_dihedral_angle_2_deg 8.808 r_long_range_B_refined 8.428 r_long_range_B_other 8.426 r_dihedral_angle_1_deg 6.732 r_scangle_other 6.078 r_mcangle_it 4.911 r_mcangle_other 4.911 r_scbond_it 3.59 r_scbond_other 3.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.034 r_dihedral_angle_2_deg 8.808 r_long_range_B_refined 8.428 r_long_range_B_other 8.426 r_dihedral_angle_1_deg 6.732 r_scangle_other 6.078 r_mcangle_it 4.911 r_mcangle_other 4.911 r_scbond_it 3.59 r_scbond_other 3.586 r_mcbond_it 3.094 r_mcbond_other 3.092 r_angle_refined_deg 1.175 r_angle_other_deg 0.373 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1375 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing