3S5Y

Pharmacological Chaperoning in Human alpha-Galactosidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HG5PDB ENTRY 3HG5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.12938-15% PEG 8000, 0.1 M Sodium Cacodylate, 0.02 M Magnesium Chloride, pH 5.1, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
3.2862.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.813α = 90
b = 182.635β = 90
c = 47.73γ = 90
Symmetry
Space GroupP 21 21 2

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
12.150950.0958.36.26677840.8
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)
12.12.1892.40.8165.86394

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3HG52.10530.4466564336094.480.19540.19360.2299RANDOM38.3445
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]
-0.70.310.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.459
r_dihedral_angle_4_deg14.117
r_dihedral_angle_3_deg13.369
r_scangle_it8.098
r_dihedral_angle_1_deg5.65
r_scbond_it5.37
r_mcangle_it3.486
r_mcbond_it2.161
r_angle_refined_deg1.126
r_mcbond_other0.825
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.459
r_dihedral_angle_4_deg14.117
r_dihedral_angle_3_deg13.369
r_scangle_it8.098
r_dihedral_angle_1_deg5.65
r_scbond_it5.37
r_mcangle_it3.486
r_mcbond_it2.161
r_angle_refined_deg1.126
r_mcbond_other0.825
r_angle_other_deg0.818
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6253
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms403

Software

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