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Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from bacillus subtilis in complex with xylotriose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W9T pdb entries 1w9t, 1gyh experimental model PDB 1GYH pdb entries 1w9t, 1gyh
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 4.0 M Na formate, 1.0 M lithium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.627 α = 90 b = 73.662 β = 90 c = 106.368 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 2007-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.0788 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 1.55 50 98.1 0.083 8.3 14 3.4 76939
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 1.55 1.58 99.9 0.322 32.2 3.9 3.1 3868
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 1w9t, 1gyh 1.55 50 73012 3871 97.85 0.16502 0.16367 0.1632 0.19007 0.192 RANDOM 16.305
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] 0.56 -0.22 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.707 r_dihedral_angle_4_deg 14.048 r_dihedral_angle_3_deg 10.53 r_dihedral_angle_1_deg 6.459 r_scangle_it 2.333 r_scbond_it 1.577 r_angle_refined_deg 1.218 r_mcangle_it 1.093 r_mcbond_it 0.631 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.707 r_dihedral_angle_4_deg 14.048 r_dihedral_angle_3_deg 10.53 r_dihedral_angle_1_deg 6.459 r_scangle_it 2.333 r_scbond_it 1.577 r_angle_refined_deg 1.218 r_mcangle_it 1.093 r_mcbond_it 0.631 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.179 r_metal_ion_refined 0.154 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3658 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MrBUMP phasing