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Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A from Ustilago maydis in complex with L-arabinofuranose
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 5 285 20% (w/v) PEG 3350 0.2 M Sodium phosphate 0.05 M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K
Crystal Properties Matthews coefficient Solvent content 1.82 32.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.08 α = 90 b = 66.07 β = 90 c = 68.1 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 ADSC QUANTUM 210 2012-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93340 ESRF ID14-1
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 1.2 50 95.9 0.026 35 4.3 85293 81763 1 -3 12.6
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 1.2 1.23 89.9 0.143 9.35 4.2 5597
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 1.2 47.42 1 81763 77664 4098 95.85 0.10118 0.09965 0.1008 0.13016 0.131 RANDOM 10.908
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] -0.01 0.04 -0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.944 r_dihedral_angle_2_deg 29.774 r_dihedral_angle_4_deg 25.815 r_dihedral_angle_3_deg 11.796 r_sphericity_bonded 10.793 r_dihedral_angle_1_deg 7.884 r_rigid_bond_restr 6.109 r_long_range_B_refined 4.768 r_long_range_B_other 3.877 r_scangle_other 3.328
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.944 r_dihedral_angle_2_deg 29.774 r_dihedral_angle_4_deg 25.815 r_dihedral_angle_3_deg 11.796 r_sphericity_bonded 10.793 r_dihedral_angle_1_deg 7.884 r_rigid_bond_restr 6.109 r_long_range_B_refined 4.768 r_long_range_B_other 3.877 r_scangle_other 3.328 r_scbond_it 2.813 r_scbond_other 2.809 r_mcbond_it 2.692 r_mcangle_other 2.679 r_mcangle_it 2.671 r_mcbond_other 2.669 r_angle_refined_deg 2.117 r_angle_other_deg 0.98 r_chiral_restr 0.128 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2376 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 29
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling