6YTP

Structure of recombinant human beta-glucocerebrosidase in complex with azide tagged cyclophellitol epoxide inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62911 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.261.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.89α = 90
b = 285.769β = 90
c = 91.674γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2016-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979490DiamondI02

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
11.768.20299.90.0770.0360.99912.15.5156446
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)
11.71.731.6140.7410.5381.15.7

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-VALUE2NT01.768.202156420784299.8610.1870.18590.212131.556
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]
4.941-2.094-2.848
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.868
r_dihedral_angle_other_1_deg30.789
r_dihedral_angle_4_deg19.613
r_dihedral_angle_3_deg13.787
r_dihedral_angle_1_deg7.293
r_lrange_other6.01
r_lrange_it6.009
r_scangle_it4.009
r_scangle_other4.009
r_mcangle_it2.989
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.868
r_dihedral_angle_other_1_deg30.789
r_dihedral_angle_4_deg19.613
r_dihedral_angle_3_deg13.787
r_dihedral_angle_1_deg7.293
r_lrange_other6.01
r_lrange_it6.009
r_scangle_it4.009
r_scangle_other4.009
r_mcangle_it2.989
r_mcangle_other2.989
r_scbond_other2.57
r_scbond_it2.569
r_mcbond_it1.976
r_mcbond_other1.975
r_angle_refined_deg1.428
r_angle_other_deg1.279
r_nbd_refined0.206
r_symmetry_nbd_other0.179
r_nbd_other0.178
r_symmetry_nbd_refined0.177
r_symmetry_xyhbond_nbd_refined0.174
r_xyhbond_nbd_refined0.165
r_nbtor_refined0.163
r_symmetry_xyhbond_nbd_other0.126
r_symmetry_nbtor_other0.08
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.007
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 Atoms661
Heterogen Atoms277

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing