9S8Y | pdb_00009s8y

Amuc1074_S1_11 in complex with N-acetyl D-glucosamine

X-RAY DIFFRACTION

---

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 E9: 30 % Precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) 0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE) 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol) 20 mg/ml Amuc1074 with 100 mM N-acetyl D-glucosamine

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.01	α = 90
b = 130.01	β = 90
c = 86.27	γ = 90

Symmetry
Space Group	I 41

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		2021-07-14	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	1.38	71.88	100	0.998	10.7	6.5		146947

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	1.38	1.4			0.707

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	1.38	41.147	146929	7209	99.963	0.168	0.1673	0.1731	0.1841	0.1902	23.564

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]
-1.328			-1.328		2.655

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.281
r_dihedral_angle_3_deg	12.709
r_dihedral_angle_1_deg	7.021
r_dihedral_angle_2_deg	6.74
r_lrange_it	5.461
r_lrange_other	5.414
r_scangle_it	4.635
r_scangle_other	4.634
r_scbond_it	3.073
r_scbond_other	3.072
r_mcangle_it	2.452
r_mcangle_other	2.452
r_angle_refined_deg	1.898
r_mcbond_it	1.741
r_mcbond_other	1.741
r_angle_other_deg	0.675
r_nbd_refined	0.225
r_nbd_other	0.19
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.182
r_metal_ion_refined	0.144
r_xyhbond_nbd_refined	0.125
r_symmetry_nbd_refined	0.104
r_chiral_restr	0.103
r_symmetry_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_symmetry_xyhbond_nbd_other	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4218
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms	46

Software

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