3LX9

Interconversion of Human Lysosomal Enzyme Specificities


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HG3PDB ENTRY 3HG3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.160.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.947α = 90
b = 139.492β = 90
c = 182.58γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315FOCUSING MIRRORS2009-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.07188APS24-ID-C

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
12.045099.40.1218.66.77200972009
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.0993.30.7010.7011.63.63354

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3HG32.0443.6971961362398.920.1780.1760.218RANDOM37.453
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.82
r_dihedral_angle_4_deg12.803
r_dihedral_angle_3_deg12.129
r_scangle_it9.8
r_scbond_it7.455
r_dihedral_angle_1_deg5.706
r_mcangle_it4.839
r_mcbond_it3.632
r_mcbond_other1.526
r_angle_refined_deg1.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.82
r_dihedral_angle_4_deg12.803
r_dihedral_angle_3_deg12.129
r_scangle_it9.8
r_scbond_it7.455
r_dihedral_angle_1_deg5.706
r_mcangle_it4.839
r_mcbond_it3.632
r_mcbond_other1.526
r_angle_refined_deg1.056
r_angle_other_deg0.964
r_chiral_restr0.099
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6241
Nucleic Acid Atoms
Solvent Atoms559
Heterogen Atoms257

Software

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