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Crystal structure of GH31 alpha-xylosidase from a soil metagenome
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 1.6 M lithium sulfate, 100 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.146 α = 90 b = 124.174 β = 116.81 c = 177.453 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 CCD RAYONIX MX300HE 2015-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 91.2 0.067 15.9 2.9 561527
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 77.2 0.252 2.8 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.8 50 533902 27623 91.12 0.17525 0.17423 0.19497 0.1778 RANDOM 17.26
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] 1.63 -0.09 -0.38 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_4_deg 13.875 r_dihedral_angle_3_deg 12.457 r_dihedral_angle_1_deg 6.373 r_long_range_B_refined 3.167 r_long_range_B_other 2.936 r_scangle_other 1.565 r_angle_refined_deg 1.295 r_mcangle_it 1.228 r_mcangle_other 1.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_4_deg 13.875 r_dihedral_angle_3_deg 12.457 r_dihedral_angle_1_deg 6.373 r_long_range_B_refined 3.167 r_long_range_B_other 2.936 r_scangle_other 1.565 r_angle_refined_deg 1.295 r_mcangle_it 1.228 r_mcangle_other 1.228 r_scbond_it 0.951 r_scbond_other 0.951 r_angle_other_deg 0.919 r_mcbond_it 0.721 r_mcbond_other 0.721 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 43498 Nucleic Acid Atoms Solvent Atoms 3729 Heterogen Atoms 312
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AutoSol phasing