9S85 | pdb_00009s85

Amuc0121_S1_15 in complex with O6 sulfated D-Galactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Morpheus D12- 37. 5 % Precipitant mix 4(25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350), 0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE), 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol). 36 mg/ml Amuc0121_C78S, 10 mM O6 sulfated D-galactose

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.055	α = 90
b = 91.127	β = 90
c = 160.101	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER2 S 16M		2025-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97625	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	60.27	100	0.996	8	13.6		1210143

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	1.8	1.83			0.446

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	60.27	88932	4555	99.998	0.187	0.185	0.193	0.2205	0.2253	25.551

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]
0.095			0.537		-0.632

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.258
r_dihedral_angle_3_deg	14.275
r_dihedral_angle_2_deg	9.991
r_dihedral_angle_1_deg	6.855
r_lrange_it	5.289
r_lrange_other	5.277
r_scangle_it	4.345
r_scangle_other	4.345
r_scbond_other	2.723
r_scbond_it	2.722
r_mcangle_it	2.432
r_mcangle_other	2.432
r_mcbond_it	1.67
r_mcbond_other	1.667
r_angle_refined_deg	1.584
r_angle_other_deg	0.545
r_symmetry_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.209
r_symmetry_nbd_other	0.197
r_nbd_other	0.182
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.125
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.074
r_metal_ion_refined	0.067
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7507
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	34

Software

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