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Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with xylotriose, calcium-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GLL
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 = 74.76 α = 90 b = 61.587 β = 95.84 c = 78.922 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 210 2015-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 99.8 0.095 21.5 7.5 78466 12.931
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 99.4 0.605 3.4 7.4
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 5GLL 1.7 78.51 74549 3854 99.73 0.15858 0.15781 0.1693 0.17352 0.1838 RANDOM 16.377
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] -0.01 -0.18 0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.652 r_dihedral_angle_4_deg 17.354 r_dihedral_angle_3_deg 11.862 r_dihedral_angle_1_deg 6.633 r_long_range_B_refined 4.302 r_long_range_B_other 4.209 r_scangle_other 1.609 r_mcangle_it 1.502 r_mcangle_other 1.502 r_angle_refined_deg 1.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.652 r_dihedral_angle_4_deg 17.354 r_dihedral_angle_3_deg 11.862 r_dihedral_angle_1_deg 6.633 r_long_range_B_refined 4.302 r_long_range_B_other 4.209 r_scangle_other 1.609 r_mcangle_it 1.502 r_mcangle_other 1.502 r_angle_refined_deg 1.267 r_scbond_it 0.951 r_scbond_other 0.951 r_angle_other_deg 0.91 r_mcbond_it 0.844 r_mcbond_other 0.841 r_chiral_restr 0.077 r_bond_refined_d 0.007 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 5190 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing