3GXT

Crystal structure of alpha-galactosidase A at pH 4.5 complexed with 1-deoxygalactonijirimycin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSIONvapor diffusion
Crystal Properties
Matthews coefficientSolvent content
2.7755.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.61α = 90
b = 89.61β = 90
c = 216.64γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.777.627633

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.719.926233140097.290.245090.241930.30577RANDOM57.738
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]
-0.14-0.07-0.140.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.935
r_dihedral_angle_3_deg21.561
r_dihedral_angle_4_deg18.923
r_dihedral_angle_1_deg9.413
r_angle_refined_deg1.95
r_scangle_it1.775
r_scbond_it1.207
r_mcangle_it0.668
r_mcbond_it0.412
r_symmetry_vdw_refined0.349
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6253
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms256

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling