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Crystal Structure of the alpha-L-arabinofuranosidase PaAbf62A from Podospora anserina
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 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.41 α = 90 b = 66.83 β = 117.39 c = 60.57 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 ADSC QUANTUM 315r 2011-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97626 ESRF ID23-1
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 1.44 45 92.3 0.045 0.045 21.86 4.56 65750 60688 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 1.44 1.48 80.3 0.093 8.26 2 3880
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 1.44 44.61 1 65231 57650 3039 92.51 0.12931 0.12812 0.1294 0.15192 0.1531 RANDOM 14.643
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] -0.03 0.05 -0.11 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_4_deg 19.686 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_1_deg 7.669 r_long_range_B_refined 6.201 r_long_range_B_other 5.866 r_scangle_other 4.064 r_scbond_it 2.823 r_scbond_other 2.823 r_mcangle_other 2.582
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_4_deg 19.686 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_1_deg 7.669 r_long_range_B_refined 6.201 r_long_range_B_other 5.866 r_scangle_other 4.064 r_scbond_it 2.823 r_scbond_other 2.823 r_mcangle_other 2.582 r_mcangle_it 2.58 r_angle_refined_deg 2.521 r_mcbond_it 1.697 r_mcbond_other 1.682 r_angle_other_deg 1.016 r_chiral_restr 0.145 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 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 2522 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 37
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling