4FDJ

The molecular basis of mucopolysaccharidosis IV A, complex with GalNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FDIPDB ENTRY 4FDI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529310-15% PEG6000, 0.1 M citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.706α = 90
b = 155.835β = 113.43
c = 61.801γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 270toroidal focusing mirror2011-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1.100NSLSX6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.85096.40.1438.62.92469039.07
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)
12.82.8583.70.2782.41055

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 4FDI2.8145.3124664126995.780.20890.20660.2509FROM PDB ENTRY 4FDI39.9954
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]
0.5-0.21-0.19-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.068
r_dihedral_angle_4_deg17.734
r_dihedral_angle_3_deg15.45
r_scangle_it5.58
r_dihedral_angle_1_deg5.523
r_scbond_it3.508
r_mcangle_it2.483
r_mcbond_it1.439
r_angle_refined_deg1.157
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.068
r_dihedral_angle_4_deg17.734
r_dihedral_angle_3_deg15.45
r_scangle_it5.58
r_dihedral_angle_1_deg5.523
r_scbond_it3.508
r_mcangle_it2.483
r_mcbond_it1.439
r_angle_refined_deg1.157
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7787
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms88

Software

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