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Crystal structure of GH146 beta-L-arabinofuranosidase Bll3HypBA1 (amino acids 380-1051), ligand-free form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 45% MPD, 0.2 M ammonium acetate, and 0.1 M HEPES-NaOH (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.231 α = 90 b = 83.51 β = 90.66 c = 102.034 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 PILATUS 6M 2016-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 1.7 49.2 99.1 0.076 0.065 0.998 7.3 3.4 137533 18.21
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 1.7 1.73 98.3 0.939 0.787 0.676 1 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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.7 43.57 130696 6825 99.15 0.2221 0.22018 0.2342 0.25941 0.2731 RANDOM 23.604
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] 0.69 1.89 -0.85 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.913 r_dihedral_angle_2_deg 8.509 r_dihedral_angle_1_deg 6.888 r_long_range_B_refined 5.034 r_long_range_B_other 5.019 r_scangle_other 3.948 r_mcangle_it 2.714 r_mcangle_other 2.713 r_scbond_it 2.528 r_scbond_other 2.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.913 r_dihedral_angle_2_deg 8.509 r_dihedral_angle_1_deg 6.888 r_long_range_B_refined 5.034 r_long_range_B_other 5.019 r_scangle_other 3.948 r_mcangle_it 2.714 r_mcangle_other 2.713 r_scbond_it 2.528 r_scbond_other 2.526 r_mcbond_it 1.836 r_mcbond_other 1.835 r_angle_refined_deg 1.328 r_angle_other_deg 0.458 r_chiral_restr 0.063 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 10440 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing