9S7X | pdb_00009s7x

Amuc0121_S1_15 in complex with 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		298	Morpheus H12- 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), 0.1 M amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine) 36 mg/ml Amuc0121 with 100 mM D-Galactose

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.51	α = 90
b = 91.49	β = 90
c = 162.08	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		2021-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.0	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	1.56	61.607	100	0.999	15.8	6.5		141184

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	1.56	1.59			0.589

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	1.56	61.607	141085	7026	99.975	0.14	0.1379	0.137	0.1843	0.1844	30.965

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]
-1.064			1.906		-0.843

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.934
r_lrange_it	15.56
r_lrange_other	15.121
r_dihedral_angle_3_deg	13.191
r_scangle_it	12.455
r_scangle_other	12.454
r_mcangle_other	9.008
r_mcangle_it	9.006
r_scbond_it	8.826
r_scbond_other	8.825
r_dihedral_angle_2_deg	6.7
r_dihedral_angle_1_deg	6.612
r_mcbond_it	6.597
r_mcbond_other	6.593
r_rigid_bond_restr	3.6
r_angle_refined_deg	1.648
r_angle_other_deg	0.581
r_nbd_other	0.237
r_nbd_refined	0.215
r_symmetry_nbd_other	0.199
r_symmetry_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.132
r_metal_ion_refined	0.104
r_symmetry_xyhbond_nbd_other	0.102
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.083
r_symmetry_nbd_refined	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7525
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	38

Software

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