7NWV

Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY Tagged Cyclophellitol activity based probe


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TJK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.5151.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.956α = 90
b = 158.42β = 102.147
c = 68.238γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976254DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.86158.421000.1190.1290.9969.16.991928
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.890.8430.9130.8592

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6TJK1.8666.891876466599.940.180.17690.231824.294
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]
0.3470.0871.848-2.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_1_deg37.453
r_dihedral_angle_2_deg34.286
r_dihedral_angle_4_deg20.072
r_dihedral_angle_3_deg14.196
r_dihedral_angle_1_deg7.478
r_lrange_it4.949
r_lrange_other4.949
r_scangle_it3.437
r_scangle_other3.437
r_scbond_it2.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_1_deg37.453
r_dihedral_angle_2_deg34.286
r_dihedral_angle_4_deg20.072
r_dihedral_angle_3_deg14.196
r_dihedral_angle_1_deg7.478
r_lrange_it4.949
r_lrange_other4.949
r_scangle_it3.437
r_scangle_other3.437
r_scbond_it2.404
r_scbond_other2.403
r_mcangle_it2.356
r_mcangle_other2.355
r_mcbond_it1.722
r_mcbond_other1.722
r_angle_refined_deg1.57
r_angle_other_deg1.329
r_nbd_other0.24
r_nbd_refined0.205
r_symmetry_nbd_refined0.192
r_symmetry_nbd_other0.187
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.162
r_symmetry_xyhbond_nbd_refined0.162
r_symmetry_nbtor_other0.092
r_chiral_restr0.08
r_symmetry_xyhbond_nbd_other0.072
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7819
Nucleic Acid Atoms
Solvent Atoms744
Heterogen Atoms384

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing