3LXA

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
3.0559.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.241α = 90
b = 104.959β = 90
c = 181.038γ = 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
13501000.2717.67.32363823638
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)
133.1199.90.8510.8511.87.22309

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 3HG33.0449.6322400112899.520.2160.2140.244RANDOM34.52
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]
-0.05-0.060.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.025
r_dihedral_angle_3_deg18.716
r_dihedral_angle_4_deg15.836
r_dihedral_angle_1_deg6
r_scangle_it5.895
r_scbond_it3.576
r_mcangle_it2.768
r_mcbond_it1.436
r_angle_refined_deg1.413
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.025
r_dihedral_angle_3_deg18.716
r_dihedral_angle_4_deg15.836
r_dihedral_angle_1_deg6
r_scangle_it5.895
r_scbond_it3.576
r_mcangle_it2.768
r_mcbond_it1.436
r_angle_refined_deg1.413
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6303
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms218

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction