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Crystal structure of fungal CE16 acetyl xylan esterase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Potassium thiocyanate, Bis Tris propane, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.74 55.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.825 α = 90 b = 91.825 β = 90 c = 162.462 γ = 120
Symmetry Space Group P 31 2 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 PILATUS 6M 2021-12-07 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) 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 1.45 162.4 100 0.99 15.5 17 140699
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 1.45 1.47 0.488
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 AlphaFold 1.45 79.65 135800 4822 100 0.14097 0.13949 0.141 0.17143 0.1416 RANDOM 24.439
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] -0.61 -0.3 -0.61 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.399 r_dihedral_angle_4_deg 17.387 r_dihedral_angle_3_deg 12.768 r_dihedral_angle_1_deg 6.541 r_long_range_B_refined 2.53 r_long_range_B_other 2.42 r_rigid_bond_restr 2.322 r_scangle_other 2.188 r_mcangle_other 1.836 r_mcangle_it 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.399 r_dihedral_angle_4_deg 17.387 r_dihedral_angle_3_deg 12.768 r_dihedral_angle_1_deg 6.541 r_long_range_B_refined 2.53 r_long_range_B_other 2.42 r_rigid_bond_restr 2.322 r_scangle_other 2.188 r_mcangle_other 1.836 r_mcangle_it 1.83 r_scbond_it 1.79 r_scbond_other 1.79 r_angle_refined_deg 1.56 r_mcbond_it 1.505 r_angle_other_deg 1.492 r_mcbond_other 1.488 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5085 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing