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Crystal structure of alkaline alpha-galctosidase D383A mutant from Arabidopsis thaliana complexed with Raffinose
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 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.603 α = 90 b = 103.301 β = 90 c = 181.436 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 PIXEL DECTRIS EIGER X 16M 2018-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.47 30 98.5 0.061 0.074 0.997 10.56 3.116 118862 67.722
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.62 96.6 0.501 0.601 0.812 1.78 3.255
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 2.47 30 59571 3170 99.27 0.1935 0.1905 0.1987 0.2488 0.1927 RANDOM 71.143
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] 6.08 -2.67 -3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.101 r_dihedral_angle_3_deg 17.979 r_dihedral_angle_4_deg 16.012 r_dihedral_angle_1_deg 8.163 r_angle_refined_deg 1.716 r_angle_other_deg 1.02 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.101 r_dihedral_angle_3_deg 17.979 r_dihedral_angle_4_deg 16.012 r_dihedral_angle_1_deg 8.163 r_angle_refined_deg 1.716 r_angle_other_deg 1.02 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 16 Heterogen Atoms 68
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction