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Crystal structure of feruloyl esterase from Fusarium oxysporum G122S variant in complex with benzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 PEG 400, Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.92 57.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.004 α = 90 b = 89.934 β = 103.767 c = 115.148 γ = 90
Symmetry Space Group P 1 21 1
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 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.71 89.93 98.6 0.065 0.09 0.062 0.995 7.5 3.4 143024
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 1.71 1.74 99.2 0.537 0.731 0.493 0.812 1.5 3.4
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 70.184 142930 7141 98.372 0.163 0.1609 0.162 0.193 0.1942 41.413
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] -0.826 4.324 -4.155 2.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.076 r_dihedral_angle_3_deg 14.265 r_dihedral_angle_2_deg 7.878 r_lrange_it 7.264 r_lrange_other 7.26 r_dihedral_angle_1_deg 6.924 r_scangle_it 5.573 r_scangle_other 5.572 r_scbond_it 3.962 r_scbond_other 3.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.076 r_dihedral_angle_3_deg 14.265 r_dihedral_angle_2_deg 7.878 r_lrange_it 7.264 r_lrange_other 7.26 r_dihedral_angle_1_deg 6.924 r_scangle_it 5.573 r_scangle_other 5.572 r_scbond_it 3.962 r_scbond_other 3.961 r_mcangle_it 3.252 r_mcangle_other 3.252 r_mcbond_it 2.591 r_mcbond_other 2.591 r_angle_refined_deg 1.99 r_angle_other_deg 0.688 r_symmetry_xyhbond_nbd_other 0.34 r_nbd_refined 0.255 r_nbd_other 0.245 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.166 r_metal_ion_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7914 Nucleic Acid Atoms Solvent Atoms 814 Heterogen Atoms 673
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PHASER phasing Aimless data scaling XDS data reduction