5FJS

Bacterial beta-glucosidase reveals the structural and functional basis of genetic defects in human glucocerebrosidase 2 (GBA2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BVUPDB ENTRY 5BVU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, PH 8, 15 % W/V PEG 6000.
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 187.974α = 90
b = 187.974β = 90
c = 99.075γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PIXEL2014-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

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
12.645.11000.1115.910.3614061.7
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)
12.62.671001.321.710.4

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 5BVU2.6162.6158306308199.970.208620.205590.26649RANDOM58.022
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]
-0.54-0.27-0.541.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.929
r_dihedral_angle_4_deg17.16
r_dihedral_angle_3_deg15.838
r_long_range_B_refined8.36
r_long_range_B_other8.354
r_dihedral_angle_1_deg7.054
r_mcangle_it6.594
r_mcangle_other6.593
r_scangle_other6.235
r_mcbond_it4.476
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.929
r_dihedral_angle_4_deg17.16
r_dihedral_angle_3_deg15.838
r_long_range_B_refined8.36
r_long_range_B_other8.354
r_dihedral_angle_1_deg7.054
r_mcangle_it6.594
r_mcangle_other6.593
r_scangle_other6.235
r_mcbond_it4.476
r_mcbond_other4.475
r_scbond_it4.208
r_scbond_other4.208
r_angle_refined_deg1.561
r_angle_other_deg1.021
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11055
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing