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Crystal structure of alkaline alpha-galactosidase D383A mutant from Arabidopsis thaliana complexed with Stachyose.
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 7.8 291.5 Tris, PEG 2000, PGA
Crystal Properties Matthews coefficient Solvent content 2.77 55.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.589 α = 90 b = 103.749 β = 90 c = 182.372 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 2018-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 0.97 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 30 99.9 0.093 0.101 0.04 7.2 6.3 124558
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 2.07 99.5 0.597 0.66 0.277 0.855 5.4
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 30 118298 6172 99.7 0.1692 0.1672 0.1765 0.2064 0.2106 RANDOM 42.678
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] -0.05 0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.385 r_dihedral_angle_4_deg 17.675 r_dihedral_angle_3_deg 16.05 r_dihedral_angle_1_deg 7.723 r_angle_refined_deg 2.01 r_angle_other_deg 1.135 r_chiral_restr 0.157 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.385 r_dihedral_angle_4_deg 17.675 r_dihedral_angle_3_deg 16.05 r_dihedral_angle_1_deg 7.723 r_angle_refined_deg 2.01 r_angle_other_deg 1.135 r_chiral_restr 0.157 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11240 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction