6Q6K

Crystal structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol activity based probe with Cy5 tag (ME569)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293Ammonium sulfate, Gaunidine Hydrochloride, Potassium chloride and Sodium acetate (pH 4.6)
Crystal Properties
Matthews coefficientSolvent content
3.2862.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.613α = 90
b = 285.934β = 90
c = 92.258γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.915870DiamondI04-1

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
11.9277.641000.195.98.4111507
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921.9599.90.7071.2

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 REPLACEMENTTHROUGHOUT2NT01.9277.64105810568099.950.186850.1850.22101RANDOM37.55
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]
5.85-1.77-4.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.921
r_dihedral_angle_4_deg18.809
r_dihedral_angle_3_deg14.775
r_long_range_B_refined7.641
r_long_range_B_other7.641
r_dihedral_angle_1_deg7.619
r_scangle_other5.478
r_mcangle_other4.294
r_mcangle_it4.293
r_scbond_it3.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.921
r_dihedral_angle_4_deg18.809
r_dihedral_angle_3_deg14.775
r_long_range_B_refined7.641
r_long_range_B_other7.641
r_dihedral_angle_1_deg7.619
r_scangle_other5.478
r_mcangle_other4.294
r_mcangle_it4.293
r_scbond_it3.64
r_scbond_other3.64
r_mcbond_it2.944
r_mcbond_other2.923
r_angle_refined_deg1.603
r_angle_other_deg1.298
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms7764
Nucleic Acid Atoms
Solvent Atoms699
Heterogen Atoms354

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing