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Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose and xylotriose, calcium-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 25% PEG 3350, 8% Tacsimate
Crystal Properties Matthews coefficient Solvent content 2.49 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.929 α = 90 b = 61.343 β = 95.79 c = 79.001 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 95 CCD ADSC QUANTUM 315 2015-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.7 100 99.9 0.075 23 7.4 78262 14.721
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 1.7 1.76 99.8 0.585 3.3 7.1
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 5GLN 1.7 78.6 74161 4084 99.82 0.15214 0.1509 0.1631 0.17465 0.1854 RANDOM 18.968
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] -0.29 0.21 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.437 r_dihedral_angle_4_deg 16.072 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 6.817 r_long_range_B_refined 4.838 r_long_range_B_other 4.761 r_scangle_other 2.447 r_mcangle_it 1.959 r_mcangle_other 1.958 r_scbond_it 1.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.437 r_dihedral_angle_4_deg 16.072 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 6.817 r_long_range_B_refined 4.838 r_long_range_B_other 4.761 r_scangle_other 2.447 r_mcangle_it 1.959 r_mcangle_other 1.958 r_scbond_it 1.473 r_scbond_other 1.47 r_angle_refined_deg 1.409 r_mcbond_it 1.154 r_mcbond_other 1.154 r_angle_other_deg 1.112 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5190 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing