3S5Z

Pharmacological Chaperoning in Human alpha-Galactosidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HG5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.1293PEG 8000, Sodium Cacodylate, Magnesium Chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1661.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.313α = 90
b = 140.606β = 90
c = 182.486γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210TOROIDAL FOCUSING MIRROR2007-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1.000NSLSX6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
125099.40.1156.513.777091
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)
122.0796.10.78210

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 REPLACEMENTTHROUGHOUT3HG52.00130.4473158386799.310.211190.209920.23436RANDOM33.715
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]
-0.050.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.394
r_dihedral_angle_3_deg13.797
r_dihedral_angle_4_deg11.718
r_scangle_it8.59
r_scbond_it6.014
r_dihedral_angle_1_deg5.785
r_mcangle_it4.002
r_mcbond_it2.624
r_angle_refined_deg1.231
r_mcbond_other0.996
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.394
r_dihedral_angle_3_deg13.797
r_dihedral_angle_4_deg11.718
r_scangle_it8.59
r_scbond_it6.014
r_dihedral_angle_1_deg5.785
r_mcangle_it4.002
r_mcbond_it2.624
r_angle_refined_deg1.231
r_mcbond_other0.996
r_angle_other_deg0.852
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6244
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms294

Software

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