9EOB | pdb_00009eob

Engineered GH181 sialidase from Akkermansia muciniphila

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8AXT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	10% PEG 8000 W/V, 9% Ethylene glycol (v/v), 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.67	α = 90
b = 88.189	β = 90
c = 99.585	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 EIGER X 16M		2024-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.98	MAX IV	BioMAX

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	1.77	66.02	99	0.998	11.7	9.6		64414

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	1.77	1.8			0.503

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	1.77	66.02	64414	3267	99.473	0.157	0.1552	0.1663	0.1953	0.2045	24.106

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]
0.045			0.647		-0.692

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.127
r_dihedral_angle_3_deg	13.187
r_dihedral_angle_1_deg	7.662
r_dihedral_angle_2_deg	6.963
r_lrange_it	6.56
r_lrange_other	6.417
r_scangle_it	5.063
r_scangle_other	5.062
r_scbond_it	3.386
r_scbond_other	3.385
r_mcangle_it	2.992
r_mcangle_other	2.992
r_mcbond_it	2.166
r_mcbond_other	2.165
r_angle_refined_deg	1.519
r_angle_other_deg	0.515
r_symmetry_nbd_refined	0.228
r_nbd_refined	0.2
r_symmetry_nbd_other	0.194
r_nbd_other	0.182
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_other	0.149
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4572
Nucleic Acid Atoms
Solvent Atoms	566
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
TRUNCATE	data scaling
MOLREP	phasing