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Crystal structure of alkaline alpha-galactosidase D383A mutant from Arabidopsis thaliana complexed with product-galactose and sucrose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291.5 Tris, PEG2000, PGA
Crystal Properties Matthews coefficient Solvent content 2.79 55.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.71 α = 90 b = 104.101 β = 90 c = 182.42 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 110 CCD RAYONIX MX300HE 2018-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 30 97.2 0.076 0.085 0.036 8.9 5.4 92281
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.717 0.789 0.327 0.88 5.6
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 7EXG 2.2 29.88 82212 4303 91.04 0.1955 0.1925 0.2014 0.2547 0.2012 RANDOM 40.111
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 19.537 r_dihedral_angle_3_deg 16.814 r_dihedral_angle_1_deg 8.356 r_angle_refined_deg 1.937 r_angle_other_deg 1.089 r_chiral_restr 0.152 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 19.537 r_dihedral_angle_3_deg 16.814 r_dihedral_angle_1_deg 8.356 r_angle_refined_deg 1.937 r_angle_other_deg 1.089 r_chiral_restr 0.152 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11242 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 70
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction