6Z39

Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY functionalised epoxide activity based probe


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.95 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
3.2762.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.172α = 90
b = 285.622β = 90
c = 91.564γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2015-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976300DiamondI03

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
11.7103.821000.090.040.99913.36159511
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)
11.71.730.9730.4450.7612

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-VALUE2NT01.7103.816159484799799.910.1630.16260.180523.297
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]
3.633-1.26-2.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.952
r_dihedral_angle_4_deg19.31
r_dihedral_angle_3_deg13.101
r_dihedral_angle_1_deg7.269
r_lrange_it4.892
r_lrange_other4.892
r_dihedral_angle_other_1_deg3.541
r_scangle_it2.943
r_scangle_other2.943
r_mcangle_it1.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.952
r_dihedral_angle_4_deg19.31
r_dihedral_angle_3_deg13.101
r_dihedral_angle_1_deg7.269
r_lrange_it4.892
r_lrange_other4.892
r_dihedral_angle_other_1_deg3.541
r_scangle_it2.943
r_scangle_other2.943
r_mcangle_it1.886
r_mcangle_other1.886
r_scbond_it1.833
r_scbond_other1.833
r_angle_refined_deg1.434
r_angle_other_deg1.288
r_mcbond_it1.186
r_mcbond_other1.185
r_dihedral_angle_other_2_deg0.803
r_symmetry_nbd_refined0.202
r_nbd_refined0.197
r_symmetry_nbd_other0.174
r_nbd_other0.168
r_nbtor_refined0.163
r_symmetry_xyhbond_nbd_refined0.159
r_symmetry_xyhbond_nbd_other0.15
r_xyhbond_nbd_refined0.148
r_chiral_restr0.095
r_symmetry_nbtor_other0.076
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7840
Nucleic Acid Atoms
Solvent Atoms904
Heterogen Atoms331

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing