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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-free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GLK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 25% PEG3350, 8% Tacsimate
Crystal Properties Matthews coefficient Solvent content 2.49 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.801 α = 90 b = 61.489 β = 95.72 c = 79.047 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 293 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 1.000 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 98.1 0.074 24.05 7.2 77216 14.789
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 84.1 0.519 3.03 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5GLK 1.7 78.65 73306 3874 98.09 0.15009 0.14876 0.17527 0.1796 RANDOM 19.184
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] -0.51 -0.63 0.01 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.223 r_dihedral_angle_4_deg 15.519 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 6.699 r_long_range_B_refined 5.072 r_long_range_B_other 4.999 r_scangle_other 2.532 r_mcangle_it 2.009 r_mcangle_other 2.009 r_scbond_it 1.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.223 r_dihedral_angle_4_deg 15.519 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 6.699 r_long_range_B_refined 5.072 r_long_range_B_other 4.999 r_scangle_other 2.532 r_mcangle_it 2.009 r_mcangle_other 2.009 r_scbond_it 1.524 r_scbond_other 1.522 r_angle_refined_deg 1.394 r_angle_other_deg 1.251 r_mcbond_it 1.178 r_mcbond_other 1.172 r_chiral_restr 0.089 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 5195 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing