6IBM

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfate ME776


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate
Crystal Properties
Matthew coefficientSolvent content
2.856.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.34α = 90
b = 90.34β = 90
c = 216γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97951DiamondI04

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
12.0778.361000.1240.0520.9989.812.263220
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)
12.072.120.7451

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 REPLACEMENTTHROUGHOUT1r462.0778.3660057307299.940.182980.180070.2416RANDOM55.243
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]
1.640.821.64-5.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.049
r_dihedral_angle_4_deg16.481
r_dihedral_angle_3_deg14.98
r_long_range_B_refined7.909
r_long_range_B_other7.908
r_dihedral_angle_1_deg7.501
r_scangle_other6.646
r_mcangle_it5.105
r_mcangle_other5.105
r_scbond_it4.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.049
r_dihedral_angle_4_deg16.481
r_dihedral_angle_3_deg14.98
r_long_range_B_refined7.909
r_long_range_B_other7.908
r_dihedral_angle_1_deg7.501
r_scangle_other6.646
r_mcangle_it5.105
r_mcangle_other5.105
r_scbond_it4.86
r_scbond_other4.859
r_mcbond_it3.897
r_mcbond_other3.893
r_angle_refined_deg1.568
r_angle_other_deg1.296
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.002
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6242
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms409

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing