7EXQ

Crystal structure of alkaline alpha-galactosidase D383A mutant from Arabidopsis thaliana complexed with product-galactose and sucrose.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7EXG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH291.5Tris, PEG2000, PGA
Crystal Properties
Matthews coefficientSolvent content
2.7955.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.71α = 90
b = 104.101β = 90
c = 182.42γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRAYONIX MX300HE2018-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.23097.20.0760.0850.0368.95.492281
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)RedundancyNumber Unique Reflections (All)
12.22.281000.7170.7890.3270.885.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7EXG2.229.8882212430391.040.19550.19250.2547RANDOM40.111
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.301
r_dihedral_angle_4_deg19.537
r_dihedral_angle_3_deg16.814
r_dihedral_angle_1_deg8.356
r_angle_refined_deg1.937
r_angle_other_deg1.089
r_chiral_restr0.152
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.301
r_dihedral_angle_4_deg19.537
r_dihedral_angle_3_deg16.814
r_dihedral_angle_1_deg8.356
r_angle_refined_deg1.937
r_angle_other_deg1.089
r_chiral_restr0.152
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11242
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms70

Software

Software
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction