6IBK

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfamidate ME763


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
2.8256.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.57α = 90
b = 90.57β = 90
c = 216.46γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.9963.591000.1090.0320.99911.512.271557
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)
11.992.030.9870.732

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 REPLACEMENTTHROUGHOUT1r461.9963.5967934349899.890.187570.184770.24394RANDOM56.986
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]
1.720.861.72-5.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.11
r_dihedral_angle_4_deg18.58
r_dihedral_angle_3_deg15.05
r_long_range_B_refined8.242
r_long_range_B_other8.242
r_dihedral_angle_1_deg7.692
r_scangle_other6.995
r_mcangle_it5.17
r_mcangle_other5.17
r_scbond_it5.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.11
r_dihedral_angle_4_deg18.58
r_dihedral_angle_3_deg15.05
r_long_range_B_refined8.242
r_long_range_B_other8.242
r_dihedral_angle_1_deg7.692
r_scangle_other6.995
r_mcangle_it5.17
r_mcangle_other5.17
r_scbond_it5.144
r_scbond_other5.144
r_mcbond_it4.022
r_mcbond_other4.018
r_angle_refined_deg1.582
r_angle_other_deg1.3
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms6245
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms402

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing