8AWK

Structure of recombinant human beta-glucocerebrosidase in complex with D-carbaxylosyl chloride


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4549.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.277α = 90
b = 76.465β = 102.047
c = 68.469γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979499DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5852.1581000.1430.9988.86.773542
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.611.5690.5631.1

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-VALUE6TN11.5852.15873507364499.9290.1530.15150.184919.369
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]
0.9790.810.23-1.425
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.482
r_dihedral_angle_4_deg19.414
r_dihedral_angle_3_deg13.163
r_dihedral_angle_1_deg7.422
r_lrange_it5.179
r_lrange_other5.178
r_scangle_it2.814
r_scangle_other2.814
r_scbond_it1.913
r_scbond_other1.912
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.482
r_dihedral_angle_4_deg19.414
r_dihedral_angle_3_deg13.163
r_dihedral_angle_1_deg7.422
r_lrange_it5.179
r_lrange_other5.178
r_scangle_it2.814
r_scangle_other2.814
r_scbond_it1.913
r_scbond_other1.912
r_mcangle_it1.717
r_mcangle_other1.717
r_angle_refined_deg1.551
r_angle_other_deg1.392
r_mcbond_it1.171
r_mcbond_other1.17
r_nbd_refined0.214
r_nbd_other0.195
r_symmetry_nbd_refined0.184
r_symmetry_xyhbond_nbd_refined0.183
r_symmetry_nbd_other0.182
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_other0.156
r_metal_ion_refined0.11
r_symmetry_nbtor_other0.092
r_chiral_restr0.078
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3926
Nucleic Acid Atoms
Solvent Atoms547
Heterogen Atoms187

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing