6IBT | pdb_00006ibt

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol aziridine ME737

X-RAY DIFFRACTION

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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
2.81	56.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.39	α = 90
b = 90.39	β = 90
c = 216.59	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		2018-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.915870	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.04	63.52	100	0.068	0.986	5.6	12.3		66254

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	2.04	2.09			0.81	0.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1r46	2.04	63.52	62943	3204	99.89	0.19811	0.19504	0.2	0.26001	0.26	RANDOM	54.268

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]
1.82	0.91		1.82		-5.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.414
r_dihedral_angle_3_deg	15.983
r_dihedral_angle_4_deg	15.054
r_long_range_B_refined	7.692
r_long_range_B_other	7.692
r_dihedral_angle_1_deg	7.652
r_scangle_other	6.276
r_mcangle_it	4.879
r_mcangle_other	4.879
r_scbond_it	4.461
r_scbond_other	4.46
r_mcbond_it	3.659
r_mcbond_other	3.648
r_angle_refined_deg	1.53
r_angle_other_deg	1.263
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
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 Atoms	Number
Protein Atoms	6242
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	317

Software

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