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Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis.
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, 30% sucrose, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.61 52.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.71 α = 90 b = 74.43 β = 90 c = 106.99 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 PIXEL PILATUS 6M 2007-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9785 SLS X10SA
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 30 96.4 0.102 10.2 14.1 4.4 35773
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) 2 2.11 93.2 0.333 33.3 3.9 4.2 4966
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 2 28.61 33849 1884 95.97 0.16994 0.16755 0.1698 0.21333 0.2153 RANDOM 16.75
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] 0.25 -1.23 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.138 r_dihedral_angle_4_deg 18.202 r_dihedral_angle_3_deg 12.757 r_dihedral_angle_1_deg 6.852 r_scangle_it 2.873 r_scbond_it 1.984 r_angle_refined_deg 1.498 r_mcangle_it 1.404 r_mcbond_it 0.832 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.138 r_dihedral_angle_4_deg 18.202 r_dihedral_angle_3_deg 12.757 r_dihedral_angle_1_deg 6.852 r_scangle_it 2.873 r_scbond_it 1.984 r_angle_refined_deg 1.498 r_mcangle_it 1.404 r_mcbond_it 0.832 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.162 r_metal_ion_refined 0.139 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3671 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing