3HG3

Human alpha-galactosidase catalytic mechanism 2. Substrate bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R46human alpha-galactosidase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293PEG8000, Magnesium acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1160.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.548α = 90
b = 106.106β = 90
c = 181.721γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.0085NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.95098.60.0880.08830.16713.89030837.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9788.40.7550.7553.19.97981

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 REPLACEMENTTHROUGHOUThuman alpha-galactosidase1.921.7190229452198.640.1670.1650.197RANDOM23.343
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]
-0.08-0.120.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.574
r_dihedral_angle_3_deg13.05
r_dihedral_angle_4_deg10.362
r_dihedral_angle_1_deg5.598
r_scangle_it4.304
r_scbond_it2.888
r_mcangle_it2.872
r_mcbond_it1.904
r_angle_refined_deg1.058
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.574
r_dihedral_angle_3_deg13.05
r_dihedral_angle_4_deg10.362
r_dihedral_angle_1_deg5.598
r_scangle_it4.304
r_scbond_it2.888
r_mcangle_it2.872
r_mcbond_it1.904
r_angle_refined_deg1.058
r_chiral_restr0.075
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6309
Nucleic Acid Atoms
Solvent Atoms893
Heterogen Atoms269

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling