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Crystal Structure of the alpha-L-arabinofuranosidase PaAbf62A from Podospora anserina in complex with cellotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N1I PDB entry 4N1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 285 25% PEG 4000, 0.2M Calcium chloride, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.27 45.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.14 α = 90 b = 66.79 β = 117.33 c = 60.36 γ = 90
Symmetry Space Group C 1 2 1
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 OXFORD ONYX CCD 2011-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Nova high-flux-micro-focus sealed tube 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 15 97.6 0.071 22 12.6 32914 32128 1 -3 12.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 87.2 0.381 2.51 5.1 2414
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 entry 4N1I 1.8 14.84 1 31794 31660 1687 99.58 0.13309 0.13113 0.1459 0.16963 0.1796 RANDOM 12.937
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.094 r_dihedral_angle_4_deg 20.583 r_dihedral_angle_3_deg 12.7 r_dihedral_angle_1_deg 7.791 r_long_range_B_other 5.508 r_long_range_B_refined 5.507 r_scangle_other 3.3 r_scbond_other 2.226 r_scbond_it 2.225 r_mcangle_other 2.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.094 r_dihedral_angle_4_deg 20.583 r_dihedral_angle_3_deg 12.7 r_dihedral_angle_1_deg 7.791 r_long_range_B_other 5.508 r_long_range_B_refined 5.507 r_scangle_other 3.3 r_scbond_other 2.226 r_scbond_it 2.225 r_mcangle_other 2.135 r_mcangle_it 2.133 r_angle_refined_deg 2.078 r_mcbond_it 1.36 r_mcbond_other 1.325 r_angle_other_deg 0.936 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.001 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 2514 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 71
Software Software Software Name Purpose CrysalisPro data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling