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Crystal structure of feruloyl esterase from Fusarium oxysporum G122S variant
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 35% (v/v) PEG400, 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.561 α = 90 b = 89.261 β = 101.725 c = 116.484 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 1.9 114.05 99.2 0.077 0.091 0.048 0.999 13 7 107339
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 1.9 1.93 99.6 1.241 1.454 0.752 0.739 1.6 7.3
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 1.9 114.05 107314 5438 99.137 0.164 0.1617 0.1645 0.1972 0.1999 41.76
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] 1.49 3.869 -3.102 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.223 r_dihedral_angle_3_deg 13.125 r_dihedral_angle_2_deg 9.857 r_dihedral_angle_1_deg 6.83 r_lrange_it 6.064 r_lrange_other 6.063 r_scangle_it 4.764 r_scangle_other 4.764 r_scbond_it 3.2 r_scbond_other 3.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.223 r_dihedral_angle_3_deg 13.125 r_dihedral_angle_2_deg 9.857 r_dihedral_angle_1_deg 6.83 r_lrange_it 6.064 r_lrange_other 6.063 r_scangle_it 4.764 r_scangle_other 4.764 r_scbond_it 3.2 r_scbond_other 3.2 r_mcangle_other 2.949 r_mcangle_it 2.948 r_mcbond_it 2.169 r_mcbond_other 2.168 r_angle_refined_deg 1.582 r_angle_other_deg 0.559 r_symmetry_nbd_refined 0.277 r_nbd_refined 0.241 r_nbd_other 0.215 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.178 r_chiral_restr 0.154 r_metal_ion_refined 0.142 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 606 Heterogen Atoms 614
Software Software Software Name Purpose REFMAC refinement PHASER phasing Aimless data scaling XDS data reduction