6YV3

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2911 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.8
Crystal Properties
Matthews coefficientSolvent content
3.2562.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.556α = 90
b = 285.273β = 90
c = 91.83γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2016-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979500DiamondI02

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
11.872.1971000.1160.0520.99810.95.9134042
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)
11.81.831001.3640.8480.591.25.8

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-VALUE2NT01.872.197134017667799.8840.1770.17550.203228.029
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]
3.874-1.618-2.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.465
r_dihedral_angle_4_deg17.405
r_dihedral_angle_3_deg13.623
r_dihedral_angle_1_deg7.172
r_lrange_it6.299
r_lrange_other6.299
r_scangle_it4.219
r_scangle_other4.219
r_mcangle_it2.914
r_mcangle_other2.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.465
r_dihedral_angle_4_deg17.405
r_dihedral_angle_3_deg13.623
r_dihedral_angle_1_deg7.172
r_lrange_it6.299
r_lrange_other6.299
r_scangle_it4.219
r_scangle_other4.219
r_mcangle_it2.914
r_mcangle_other2.914
r_scbond_it2.638
r_scbond_other2.638
r_mcbond_it1.871
r_mcbond_other1.87
r_dihedral_angle_other_1_deg1.632
r_angle_refined_deg1.443
r_angle_other_deg1.295
r_symmetry_nbd_refined0.214
r_nbd_refined0.204
r_nbd_other0.201
r_symmetry_nbd_other0.187
r_xyhbond_nbd_refined0.165
r_nbtor_refined0.164
r_symmetry_xyhbond_nbd_refined0.137
r_symmetry_nbtor_other0.08
r_chiral_restr0.073
r_symmetry_xyhbond_nbd_other0.026
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 Atoms7791
Nucleic Acid Atoms
Solvent Atoms855
Heterogen Atoms269

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing