4FNS

Crystal structure of GH36 alpha-galactosidase AgaA A355E from Geobacillus stearothermophilus in complex with 1-deoxygalactonojirimycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MI6PDB ID 3MI6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.829220% PEG 3350, 0.2M Potassium nitrate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2846.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.3α = 90
b = 150.3β = 90
c = 233.36γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42011-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-41.18ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.65097.50.07211.352.19421691886-332.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6796.70.3132.2

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ID 3MI62.649.1971.999188691886459697.610.17670.17380.231
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]
0.87590.8759-1.7517
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.911
f_angle_d0.609
f_chiral_restr0.044
f_bond_d0.002
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23148
Nucleic Acid Atoms
Solvent Atoms980
Heterogen Atoms88

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling