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Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 120 seconds
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KJ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.16 13% PEG3350, 0.1 M Tris-HCl pH8.5, 0.2% MgCl2
Crystal Properties Matthews coefficient Solvent content 3.43 64.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.429 α = 90 b = 89.23 β = 90 c = 218.087 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2018-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.068 158.24 95.1 0.112 0.132 0.067 30.8 3.5 257788
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 2.068 2.11 0.913 0.555 0.584 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6KJ0 2.07 35.97 245068 12720 94.96 0.22109 0.21913 0.2307 0.25895 0.2683 RANDOM 39.556
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] -2.98 5.48 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.35 r_dihedral_angle_2_deg 9.968 r_dihedral_angle_1_deg 7.47 r_long_range_B_refined 7.461 r_long_range_B_other 7.449 r_scangle_other 5.488 r_mcangle_it 5.002 r_mcangle_other 5.002 r_scbond_it 3.563 r_scbond_other 3.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.35 r_dihedral_angle_2_deg 9.968 r_dihedral_angle_1_deg 7.47 r_long_range_B_refined 7.461 r_long_range_B_other 7.449 r_scangle_other 5.488 r_mcangle_it 5.002 r_mcangle_other 5.002 r_scbond_it 3.563 r_scbond_other 3.563 r_mcbond_it 3.317 r_mcbond_other 3.316 r_angle_refined_deg 1.532 r_angle_other_deg 0.517 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 24034 Nucleic Acid Atoms Solvent Atoms 1294 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing