4DO5

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 = 154.352α = 90
b = 114.513β = 95.64
c = 68.553γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210TOROIDAL FOCUSING MIRROR2008-10-12MSINGLE 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)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
11.55096.10.0460.04615.34178912
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)
11.51.5573.20.6442.913588

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 3H531.5131.89178628902195.570.16010.15920.1779RANDOM29.5642
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]
-0.020.18-0.050.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.257
r_dihedral_angle_4_deg18.342
r_dihedral_angle_3_deg12.461
r_scangle_it8.533
r_dihedral_angle_1_deg6.291
r_scbond_it5.924
r_mcangle_it3.859
r_mcbond_it2.627
r_angle_refined_deg1.361
r_mcbond_other1.047
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.257
r_dihedral_angle_4_deg18.342
r_dihedral_angle_3_deg12.461
r_scangle_it8.533
r_dihedral_angle_1_deg6.291
r_scbond_it5.924
r_mcangle_it3.859
r_mcbond_it2.627
r_angle_refined_deg1.361
r_mcbond_other1.047
r_angle_other_deg0.886
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms1022
Heterogen Atoms338

Software

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