Experiment: 9AVS

Human alpha-galactosidase A in complex with saposin B

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S5Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	500 nL of protein (0.1 mM GLA plus 0.22 mM SapB) was mixed with 500 nL of reservoir solution (0.1 M Tris pH 8.0, 1 M Ammonium sulfate) and equilibrated against 70 uL reservoirs at 20 C.

Crystal Properties
Matthews coefficient	Solvent content
4.18	70.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.116	α = 90
b = 142.563	β = 90
c = 191.967	γ = 90

Symmetry
Space Group	C 2 2 21

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		2019-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.53	57.23	99	0.237	0.997	7.12	12.9		20451			90.16

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.53	3.656	99.8		1.057	0.903	1.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.53	57.23	1.35	20423	1009	99.04	0.2417	0.2406	0.2412	0.2648	0.2666	95.49

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.9521
f_angle_d	0.725
f_chiral_restr	0.0486
f_plane_restr	0.0061
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6848
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	303

Software

Software
Software Name	Purpose
PHASER	phasing
PHENIX	refinement
xia2	data reduction
xia2	data scaling