6TJQ

Crystal Structure of Recombinant GBA in Complex with 2-Deoxy-2-fluoro-beta-D-glucopyranoside


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4349.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.112α = 90
b = 76.351β = 101.987
c = 68.16γ = 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 I040.9795DiamondI04

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
11.4151.951000.1350.0560.9997.26.7102363
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.417.722.3880.3570.4

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-VALUE6TJK1.4151.95102326499299.90.1790.17760.205320.829
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]
0.4620.7481.266-1.876
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.684
r_dihedral_angle_4_deg20.58
r_dihedral_angle_1_deg18.896
r_dihedral_angle_3_deg13.019
r_lrange_it4.66
r_lrange_other4.399
r_scangle_it2.596
r_scangle_other2.595
r_scbond_it1.742
r_scbond_other1.741
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.684
r_dihedral_angle_4_deg20.58
r_dihedral_angle_1_deg18.896
r_dihedral_angle_3_deg13.019
r_lrange_it4.66
r_lrange_other4.399
r_scangle_it2.596
r_scangle_other2.595
r_scbond_it1.742
r_scbond_other1.741
r_mcangle_it1.637
r_mcangle_other1.637
r_angle_refined_deg1.461
r_angle_other_deg1.358
r_mcbond_it1.136
r_mcbond_other1.136
r_nbd_other0.234
r_nbd_refined0.208
r_symmetry_nbd_other0.179
r_symmetry_xyhbond_nbd_refined0.174
r_symmetry_nbd_refined0.172
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_other0.164
r_xyhbond_nbd_refined0.161
r_symmetry_nbtor_other0.096
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3923
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms177

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing