6YTR

Structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol aziridine inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NT0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.0759.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.155α = 90
b = 156.779β = 102.116
c = 68.23γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9762DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
11.766.79999.90.1590.0640.9946.36.6119361
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7399.71.831.070.5471

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-VALUE2NT01.766.799119361592799.8830.1610.15920.202624.919
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]
0.6590.1440.625-1.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_1_deg48.62
r_dihedral_angle_2_deg33.948
r_dihedral_angle_4_deg19.2
r_dihedral_angle_3_deg13.438
r_dihedral_angle_1_deg7.497
r_lrange_it5.163
r_lrange_other5.162
r_scangle_it3.628
r_scangle_other3.628
r_scbond_it2.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_1_deg48.62
r_dihedral_angle_2_deg33.948
r_dihedral_angle_4_deg19.2
r_dihedral_angle_3_deg13.438
r_dihedral_angle_1_deg7.497
r_lrange_it5.163
r_lrange_other5.162
r_scangle_it3.628
r_scangle_other3.628
r_scbond_it2.57
r_scbond_other2.57
r_mcangle_it2.301
r_mcangle_other2.3
r_mcbond_it1.704
r_mcbond_other1.704
r_angle_refined_deg1.591
r_angle_other_deg1.372
r_nbd_other0.31
r_symmetry_nbd_refined0.245
r_symmetry_xyhbond_nbd_refined0.224
r_nbd_refined0.209
r_symmetry_nbd_other0.182
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.164
r_metal_ion_refined0.163
r_symmetry_xyhbond_nbd_other0.108
r_symmetry_nbtor_other0.092
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7833
Nucleic Acid Atoms
Solvent Atoms877
Heterogen Atoms360

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing