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exo-beta-D-arabinanase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with Tris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.9 293.15 0.18 M MgCl2, 0.1 M Tris-HCl (pH 9.0), 14% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.552 α = 90 b = 97.511 β = 100.55 c = 139.978 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 PILATUS3 6M 2022-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 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 48.76 100 0.046 0.043 0.874 14.8 3.4 176777 14.64
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 0.366 0.246 0.873 2.9
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 48.8 167894 8854 99.95 0.13941 0.13757 0.1509 0.17386 0.1843 RANDOM 19.794
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] -1.26 1.54 -1.11 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.668 r_dihedral_angle_2_deg 12.595 r_dihedral_angle_1_deg 7.389 r_long_range_B_refined 5.352 r_long_range_B_other 5.351 r_scangle_other 4.355 r_scbond_it 3.188 r_scbond_other 3.188 r_mcangle_it 2.78 r_mcangle_other 2.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.668 r_dihedral_angle_2_deg 12.595 r_dihedral_angle_1_deg 7.389 r_long_range_B_refined 5.352 r_long_range_B_other 5.351 r_scangle_other 4.355 r_scbond_it 3.188 r_scbond_other 3.188 r_mcangle_it 2.78 r_mcangle_other 2.78 r_mcbond_it 2.169 r_mcbond_other 2.169 r_angle_refined_deg 1.881 r_angle_other_deg 1.327 r_chiral_restr 0.102 r_gen_planes_other 0.029 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.002 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 13230 Nucleic Acid Atoms Solvent Atoms 1661 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing