6Z3I

Structure of recombinant beta-glucocerebrosidase in complex with bifunctional cyclophellitol aziridine activity based probe


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TJK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.2 M Na2SO4, 0.25 M HEPES pH 7, PEG3350 14%, 1:1000 seed
Crystal Properties
Matthews coefficientSolvent content
2.4349.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.139α = 90
b = 76.67β = 102.053
c = 67.988γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979507DiamondI04

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
11.876.671000.2070.0840.9956.7749541
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)
11.81.841002.3511.3010.5060.86.8

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-VALUE6TJK1.866.57849519250999.9620.1790.17820.189425.448
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]
1.8321.1530.507-2.595
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.291
r_dihedral_angle_4_deg19.941
r_dihedral_angle_3_deg13.025
r_dihedral_angle_1_deg7.487
r_lrange_it3.832
r_lrange_other3.666
r_scangle_it2.355
r_scangle_other2.355
r_mcangle_it1.634
r_mcangle_other1.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.291
r_dihedral_angle_4_deg19.941
r_dihedral_angle_3_deg13.025
r_dihedral_angle_1_deg7.487
r_lrange_it3.832
r_lrange_other3.666
r_scangle_it2.355
r_scangle_other2.355
r_mcangle_it1.634
r_mcangle_other1.634
r_scbond_it1.523
r_scbond_other1.523
r_angle_refined_deg1.388
r_angle_other_deg1.25
r_mcbond_it1.072
r_mcbond_other1.069
r_nbd_other0.234
r_symmetry_nbd_refined0.219
r_nbd_refined0.203
r_symmetry_nbd_other0.178
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.165
r_symmetry_xyhbond_nbd_refined0.151
r_symmetry_xyhbond_nbd_other0.097
r_symmetry_nbtor_other0.083
r_chiral_restr0.067
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3922
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms189

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing