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Crystal structure of barley exohydrolase isoform ExoI E220A mutant in complex with 2-deoxy-2-fluoro-D-glucopyranosides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WLI 3WLI is recombinant wild-type protein ligand-free protein experimental model PDB 1IEW 1IEW contains native wild-type protein in complex with G2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 1.7 M ammonium sulfate, 75 mM HEPES-NaOH buffer, pH 7, containing 7.5 mM sodium acetate and 1.2% (w/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 3.5 64.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.5 α = 90 b = 100.5 β = 90 c = 182.689 γ = 90
Symmetry Space Group P 43 21 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 CCD ADSC QUANTUM 210r COLLIMATING MIRROR 2010-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.95 88.06 100 0.997 38.7 28.2 64687
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.997
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 3WLI 1.95 88.06 64687 3452 99.32 0.14572 0.14368 0.1575 0.18406 0.1924 RANDOM 38.339
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] 1.49 1.49 -2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.923 r_dihedral_angle_4_deg 19.229 r_dihedral_angle_3_deg 13.147 r_long_range_B_refined 7.281 r_dihedral_angle_1_deg 7.207 r_long_range_B_other 6.978 r_scangle_other 5.563 r_scbond_it 4.375 r_scbond_other 4.126 r_mcangle_other 3.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.923 r_dihedral_angle_4_deg 19.229 r_dihedral_angle_3_deg 13.147 r_long_range_B_refined 7.281 r_dihedral_angle_1_deg 7.207 r_long_range_B_other 6.978 r_scangle_other 5.563 r_scbond_it 4.375 r_scbond_other 4.126 r_mcangle_other 3.145 r_mcangle_it 3.144 r_mcbond_it 2.704 r_mcbond_other 2.577 r_angle_refined_deg 2.512 r_angle_other_deg 1.629 r_chiral_restr 0.162 r_bond_refined_d 0.029 r_gen_planes_refined 0.015 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4592 Nucleic Acid Atoms Solvent Atoms 629 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing