6TJK

Crystal Structure of Recombinant GBA in Complex with Bis-Tris Propane.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q6K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2 M Na2SO4, 14% (v/v) PEG3350, 0.1 M bis-tris-propane pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4750.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.744α = 90
b = 156.222β = 102.473
c = 68.264γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-07-19MSINGLE 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
11.5666.74299.40.1050.0570.9877.44.3147746
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)
11.561.591.670.9010.3360.7

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-VALUE6Q6K1.5666.742147674746596.7140.1660.16460.198522.553
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]
1.4570.66-0.632-1.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.465
r_dihedral_angle_4_deg18.972
r_dihedral_angle_3_deg13.019
r_dihedral_angle_1_deg7.472
r_lrange_it4.783
r_lrange_other4.779
r_scangle_it3.369
r_scangle_other3.368
r_scbond_it2.37
r_scbond_other2.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.465
r_dihedral_angle_4_deg18.972
r_dihedral_angle_3_deg13.019
r_dihedral_angle_1_deg7.472
r_lrange_it4.783
r_lrange_other4.779
r_scangle_it3.369
r_scangle_other3.368
r_scbond_it2.37
r_scbond_other2.37
r_mcangle_it2.15
r_mcangle_other2.15
r_angle_refined_deg1.588
r_mcbond_it1.579
r_mcbond_other1.576
r_angle_other_deg1.394
r_nbd_other0.236
r_nbd_refined0.214
r_symmetry_nbd_other0.192
r_symmetry_xyhbond_nbd_refined0.181
r_xyhbond_nbd_refined0.177
r_nbtor_refined0.171
r_chiral_restr_other0.166
r_symmetry_nbd_refined0.149
r_symmetry_nbtor_other0.094
r_chiral_restr0.084
r_symmetry_xyhbond_nbd_other0.016
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7833
Nucleic Acid Atoms
Solvent Atoms895
Heterogen Atoms411

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing