4DO6

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
3.2762.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.309α = 90
b = 114.304β = 96.43
c = 68.574γ = 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
11.65094.70.060.0612.96145750
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)
11.61.6363.80.6534.24888

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 3H531.643.79145693738294.670.15450.15360.1704RANDOM30.9869
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]
0.120.2-0.05-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.508
r_dihedral_angle_4_deg18.122
r_dihedral_angle_3_deg12.095
r_scangle_it8.566
r_dihedral_angle_1_deg6.106
r_scbond_it5.806
r_mcangle_it4.054
r_mcbond_it2.593
r_angle_refined_deg1.244
r_mcbond_other1.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.508
r_dihedral_angle_4_deg18.122
r_dihedral_angle_3_deg12.095
r_scangle_it8.566
r_dihedral_angle_1_deg6.106
r_scbond_it5.806
r_mcangle_it4.054
r_mcbond_it2.593
r_angle_refined_deg1.244
r_mcbond_other1.038
r_angle_other_deg0.854
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6287
Nucleic Acid Atoms
Solvent Atoms786
Heterogen Atoms294

Software

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