3LXB

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
3.1560.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.79α = 90
b = 106.996β = 90
c = 181.598γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315TOROIDAL FOCUSING MIRROR2009-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.98010NSLSX6A

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
12.855099.50.1779.14.92789727897
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)
12.852.999.90.6160.6162.24.91334

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 3HG32.8545.2727799135299.30.2270.2250.264RANDOM32.493
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]
-0.10.26-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.224
r_dihedral_angle_4_deg18.444
r_dihedral_angle_3_deg16.935
r_dihedral_angle_1_deg5.364
r_scangle_it3.438
r_mcangle_it3.204
r_scbond_it2.197
r_mcbond_it1.89
r_angle_refined_deg1.222
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.224
r_dihedral_angle_4_deg18.444
r_dihedral_angle_3_deg16.935
r_dihedral_angle_1_deg5.364
r_scangle_it3.438
r_mcangle_it3.204
r_scbond_it2.197
r_mcbond_it1.89
r_angle_refined_deg1.222
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6320
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms206

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction