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Crystal structure of GH146 beta-L-arabinofuranosidase Bll3HypBA1 (amino acids 380-1223) in complex with Tris
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 12% PEG 8000, 0.2 M MgCl2, and 0.1 M Tris-HCl (pH 8.5)
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.592 α = 90 b = 111.571 β = 90 c = 153.01 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 PILATUS 2M-F 2016-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 49.76 100 0.176 0.102 0.993 8.9 6.7 103620 5.03
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 1.014 0.592 0.696 6.8
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 1.75 49.76 98241 5288 99.99 0.14414 0.14289 0.1573 0.1673 0.1761 RANDOM 12.145
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] -0.78 -0.19 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.14 r_dihedral_angle_2_deg 9.623 r_dihedral_angle_1_deg 6.316 r_long_range_B_other 6.05 r_long_range_B_refined 6.048 r_scangle_other 4.425 r_scbond_it 2.874 r_scbond_other 2.874 r_mcangle_other 1.648 r_mcangle_it 1.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.14 r_dihedral_angle_2_deg 9.623 r_dihedral_angle_1_deg 6.316 r_long_range_B_other 6.05 r_long_range_B_refined 6.048 r_scangle_other 4.425 r_scbond_it 2.874 r_scbond_other 2.874 r_mcangle_other 1.648 r_mcangle_it 1.646 r_angle_refined_deg 1.64 r_mcbond_it 1.134 r_mcbond_other 1.124 r_angle_other_deg 0.582 r_chiral_restr 0.087 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_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 5227 Nucleic Acid Atoms Solvent Atoms 942 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing