6IBM

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R46

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.34	α = 90
b = 90.34	β = 90
c = 216	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2018-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97951	Diamond	I04

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.07	78.36	100	0.124	0.052	0.998	9.8	12.2		63220

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.12			0.745	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1r46	2.07	78.36	60057	3072	99.94	0.18298	0.18007	0.2416	RANDOM	55.243

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]
1.64	0.82		1.64		-5.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.049
r_dihedral_angle_4_deg	16.481
r_dihedral_angle_3_deg	14.98
r_long_range_B_refined	7.909
r_long_range_B_other	7.908
r_dihedral_angle_1_deg	7.501
r_scangle_other	6.646
r_mcangle_it	5.105
r_mcangle_other	5.105
r_scbond_it	4.86
r_scbond_other	4.859
r_mcbond_it	3.897
r_mcbond_other	3.893
r_angle_refined_deg	1.568
r_angle_other_deg	1.296
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	6242
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	409

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing