6TN1

Unliganded Crystal Structure of Recombinant GBA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NT1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Mg formate, 19% (v/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2745.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.451α = 86.04
b = 46.176β = 75.191
c = 64.209γ = 82.782
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

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
10.9831.6874.20.0430.0370.9948.71.9208682
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)
10.9810.4860.4860.685

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-VALUE2NT10.9831.68208659982974.2350.1120.11160.12829.105
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]
0.2390.025-0.2490.065-0.348-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.052
r_dihedral_angle_4_deg18.453
r_dihedral_angle_3_deg12.571
r_dihedral_angle_1_deg6.998
r_lrange_it2.461
r_lrange_other2.405
r_angle_refined_deg1.568
r_angle_other_deg1.513
r_scangle_it1.154
r_scangle_other1.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.052
r_dihedral_angle_4_deg18.453
r_dihedral_angle_3_deg12.571
r_dihedral_angle_1_deg6.998
r_lrange_it2.461
r_lrange_other2.405
r_angle_refined_deg1.568
r_angle_other_deg1.513
r_scangle_it1.154
r_scangle_other1.154
r_rigid_bond_restr0.995
r_mcangle_it0.937
r_mcangle_other0.937
r_scbond_it0.926
r_scbond_other0.926
r_mcbond_it0.663
r_mcbond_other0.663
r_nbd_refined0.266
r_symmetry_xyhbond_nbd_other0.254
r_nbd_other0.241
r_xyhbond_nbd_refined0.211
r_symmetry_nbd_refined0.2
r_symmetry_nbd_other0.192
r_nbtor_refined0.178
r_symmetry_xyhbond_nbd_refined0.169
r_chiral_restr0.087
r_symmetry_nbtor_other0.081
r_metal_ion_refined0.041
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3909
Nucleic Acid Atoms
Solvent Atoms693
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing