3H54

Crystal Structure of human alpha-N-acetylgalactosaminidase,complex with GalNAc


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.1293PEG3350, citric acid, Bis-Tris propane, pH 4.1, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2762.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.354α = 90
b = 114.159β = 95.62
c = 68.342γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic Blue2008-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
12.25099.10.10615.965920554.3
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)
12.22.2895.90.67424.25733

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 3H532.239.0159203298498.660.1670.1650.205RANDOM36.6
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]
-0.06-0.01-0.070.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.48
r_dihedral_angle_4_deg18.783
r_dihedral_angle_3_deg13.709
r_dihedral_angle_1_deg5.732
r_scangle_it4.833
r_mcangle_it3.55
r_scbond_it3.42
r_mcbond_it2.503
r_angle_refined_deg1.109
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.48
r_dihedral_angle_4_deg18.783
r_dihedral_angle_3_deg13.709
r_dihedral_angle_1_deg5.732
r_scangle_it4.833
r_mcangle_it3.55
r_scbond_it3.42
r_mcbond_it2.503
r_angle_refined_deg1.109
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6162
Nucleic Acid Atoms
Solvent Atoms655
Heterogen Atoms357

Software

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