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STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A FROM FUSARIUM GRAMINEARUM IN COMPLEX WITH AN hydroximolactone INHIBITOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 40% peg550MME 0.1M mes 6.5 0.2M MnSO4
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.222 α = 90 b = 105.222 β = 90 c = 140.234 γ = 90
Symmetry Space Group I 41 2 2
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 DECTRIS PILATUS 2M 2014-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.12713 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 35.06 99.3 0.12 11.1 7.1 26709 2 15.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.8 0.561 3.6 7.2
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 2YDT 2 35.06 25290 1402 99.1 0.148 0.146 0.1572 0.192 0.1994 RANDOM 20.24
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] 0.44 0.44 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.392 r_dihedral_angle_4_deg 15.407 r_dihedral_angle_3_deg 12.129 r_dihedral_angle_1_deg 7.105 r_long_range_B_refined 4.961 r_long_range_B_other 4.852 r_scangle_other 3.284 r_mcangle_other 2.244 r_mcangle_it 2.242 r_scbond_it 2.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.392 r_dihedral_angle_4_deg 15.407 r_dihedral_angle_3_deg 12.129 r_dihedral_angle_1_deg 7.105 r_long_range_B_refined 4.961 r_long_range_B_other 4.852 r_scangle_other 3.284 r_mcangle_other 2.244 r_mcangle_it 2.242 r_scbond_it 2.152 r_scbond_other 2.152 r_angle_refined_deg 1.785 r_mcbond_it 1.484 r_mcbond_other 1.471 r_angle_other_deg 0.994 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 2825 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing