3HG4

Human alpha-galactosidase catalytic mechanism 3. Covalent intermediate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.856.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.218α = 90
b = 90.218β = 90
c = 216.615γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic BlueMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
12.35099.70.1120.11228.32815.94633751.2
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)
12.32.381000.9440.9443.4164548

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUThuman alpha-galactosidase2.318.054626894999.860.1660.1650.221RANDOM49.847
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.363
r_dihedral_angle_3_deg14.292
r_dihedral_angle_4_deg13.572
r_dihedral_angle_1_deg5.882
r_scangle_it1.828
r_angle_refined_deg1.159
r_scbond_it1.058
r_mcangle_it0.609
r_mcbond_it0.375
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.363
r_dihedral_angle_3_deg14.292
r_dihedral_angle_4_deg13.572
r_dihedral_angle_1_deg5.882
r_scangle_it1.828
r_angle_refined_deg1.159
r_scbond_it1.058
r_mcangle_it0.609
r_mcbond_it0.375
r_nbtor_refined0.306
r_nbd_refined0.186
r_symmetry_vdw_refined0.168
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.121
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6261
Nucleic Acid Atoms
Solvent Atoms682
Heterogen Atoms307

Software

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