6IBR

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol epoxide LWA481


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R46 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.8156.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.38α = 90
b = 90.38β = 90
c = 216.25γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
12.0263.481000.1240.0510.99911.712.268088
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.022.070.822

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1r462.0263.4864680331499.890.197230.194330.25569RANDOM51.353
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]
1.70.851.7-5.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.51
r_dihedral_angle_3_deg15.927
r_dihedral_angle_4_deg15.154
r_dihedral_angle_1_deg7.592
r_long_range_B_refined7.463
r_long_range_B_other7.462
r_scangle_other5.906
r_mcangle_it4.651
r_mcangle_other4.651
r_scbond_it4.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.51
r_dihedral_angle_3_deg15.927
r_dihedral_angle_4_deg15.154
r_dihedral_angle_1_deg7.592
r_long_range_B_refined7.463
r_long_range_B_other7.462
r_scangle_other5.906
r_mcangle_it4.651
r_mcangle_other4.651
r_scbond_it4.226
r_scbond_other4.226
r_mcbond_it3.461
r_mcbond_other3.453
r_angle_refined_deg1.545
r_angle_other_deg1.281
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6229
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms345

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing