4DO4

Pharmacological chaperones for human alpha-N-acetylgalactosaminidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H53PDB entry 3H53

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.42938-16% PEG3350, 70mM citric acid, 30mM Bis-Tris propane, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3162.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.055α = 90
b = 114.624β = 95.82
c = 68.63γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315PT COATED MIRROR2010-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.100NSLSX25

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
11.45098.90.0580.05813.65.1228468
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)
11.41.4294.90.842410879

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 SYNTHESISTHROUGHOUTPDB entry 3H531.426.632282681148198.590.14330.14150.1776RANDOM31.11
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]
0.020.05-0.050.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.79
r_dihedral_angle_4_deg18.715
r_scangle_it13.901
r_dihedral_angle_3_deg12.647
r_scbond_it10.819
r_mcangle_it7.373
r_dihedral_angle_1_deg6.186
r_mcbond_it5.886
r_rigid_bond_restr2.78
r_mcbond_other2.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.79
r_dihedral_angle_4_deg18.715
r_scangle_it13.901
r_dihedral_angle_3_deg12.647
r_scbond_it10.819
r_mcangle_it7.373
r_dihedral_angle_1_deg6.186
r_mcbond_it5.886
r_rigid_bond_restr2.78
r_mcbond_other2.365
r_angle_refined_deg1.457
r_angle_other_deg0.927
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6279
Nucleic Acid Atoms
Solvent Atoms991
Heterogen Atoms363

Software

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