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Acetyl xylan esterase B from Aspergillus oryzae (AoAXEB), apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M Potassium fluoride, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.614 α = 90 b = 63.529 β = 90 c = 83.417 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2021-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 47.45 100 0.117 0.049 0.998 12.1 6.6 31605 9.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.859 0.379 0.713 2.1 6
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 (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 1.75 47.45 29987 1562 100 0.16601 0.16437 0.1768 0.19893 0.2089 RANDOM 17.148
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] 0.23 -0.5 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.373 r_dihedral_angle_4_deg 21.518 r_dihedral_angle_3_deg 12.361 r_dihedral_angle_1_deg 7.291 r_long_range_B_refined 5.341 r_long_range_B_other 5.174 r_scangle_other 3.776 r_scbond_it 2.472 r_scbond_other 2.471 r_mcangle_it 2.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.373 r_dihedral_angle_4_deg 21.518 r_dihedral_angle_3_deg 12.361 r_dihedral_angle_1_deg 7.291 r_long_range_B_refined 5.341 r_long_range_B_other 5.174 r_scangle_other 3.776 r_scbond_it 2.472 r_scbond_other 2.471 r_mcangle_it 2.267 r_mcangle_other 2.267 r_angle_refined_deg 1.669 r_mcbond_it 1.543 r_mcbond_other 1.54 r_angle_other_deg 1.444 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2312 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MoRDa phasing