2E9M

Crystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related Prote:KLrP) complex with Galactose and fatty acids


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E9LPDB ENTRY 2E9L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293.427.5% PEG3350, 0.1M Tris-HCl buffer, pH 8.5, 0.2M magnesium chloride, 5% glycerol, 0.5M galactose, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K
Crystal Properties
Matthews coefficientSolvent content
2.4249.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.244α = 90
b = 83.797β = 90
c = 93.591γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102006-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.85085.30.0570.05735.77.14077640776
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)
1.81.8699.90.3210.3216.77.24816

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2E9L1.838.213804238042200681.880.203150.203150.201330.23642RANDOM21.962
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]
0.030.03-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.267
r_dihedral_angle_4_deg19.075
r_dihedral_angle_3_deg13.609
r_dihedral_angle_1_deg6.131
r_scangle_it2.172
r_scbond_it1.381
r_angle_refined_deg1.183
r_mcangle_it0.899
r_mcbond_it0.539
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.267
r_dihedral_angle_4_deg19.075
r_dihedral_angle_3_deg13.609
r_dihedral_angle_1_deg6.131
r_scangle_it2.172
r_scbond_it1.381
r_angle_refined_deg1.183
r_mcangle_it0.899
r_mcbond_it0.539
r_nbtor_refined0.306
r_nbd_refined0.195
r_symmetry_vdw_refined0.158
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.128
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3782
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing