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Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis in complex with xylotetraose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GYH pdb entries 1gyh, 1w9t experimental model PDB 1W9T pdb entries 1gyh, 1w9t
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 4.0 M Na formate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.523 α = 90 b = 72.401 β = 90 c = 106.869 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.0322 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.02 50 97 0.046 4.6 4.5 33537
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.09 93.9 0.137 13.7 8 4.2 1596
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 pdb entries 1gyh, 1w9t 2.02 31.96 31709 1788 95.17 0.145 0.14262 0.1443 0.1874 0.1873 RANDOM 13.734
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] 0.18 -0.35 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.384 r_dihedral_angle_1_deg 20.515 r_dihedral_angle_4_deg 17.598 r_dihedral_angle_3_deg 12.429 r_scangle_it 2.774 r_scbond_it 1.896 r_angle_refined_deg 1.763 r_mcangle_it 1.356 r_mcbond_it 0.771 r_symmetry_hbond_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.384 r_dihedral_angle_1_deg 20.515 r_dihedral_angle_4_deg 17.598 r_dihedral_angle_3_deg 12.429 r_scangle_it 2.774 r_scbond_it 1.896 r_angle_refined_deg 1.763 r_mcangle_it 1.356 r_mcbond_it 0.771 r_symmetry_hbond_refined 0.324 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.167 r_metal_ion_refined 0.161 r_chiral_restr 0.122 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3664 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing