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Crystal structure of barley exohydrolaseI W434Y in complex with 4'-nitrophenyl thiolaminaribioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 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 3.44 64.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.471 α = 90 b = 100.471 β = 90 c = 179.807 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 2012-11-22 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) 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 2.25 87.71 99.8 0.158 26.4 29 42365
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 2.25 2.3 0.875
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 2.25 45.85 42365 2248 99.77 0.16495 0.1627 0.1738 0.20751 0.216 RANDOM 32.965
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] 0.16 0.16 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.724 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 15.343 r_dihedral_angle_1_deg 7.91 r_angle_refined_deg 1.99 r_angle_other_deg 1.444 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.724 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 15.343 r_dihedral_angle_1_deg 7.91 r_angle_refined_deg 1.99 r_angle_other_deg 1.444 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4569 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing