Experiment: 9FYO

Lacto-N-biosidase from Trueperella pyogenes

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	8.5	294.15	0,01 M Nickel II chloride hexahydrate, 0,1M Tris pH8,5 and 20% PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.759	α = 90
b = 93.686	β = 90
c = 94.037	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 PILATUS 6M		2022-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.6888	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.77	65.3	98.46	0.083	0.024	0.999	20.31	13.4		20739			77.92

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.77	2.86			1	0.281	0.89

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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.77	65.3	1.35	20733	1083	98.48	0.2292	0.2272	0.2681	0.2584	88.45

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	7.7876
f_angle_d	1.6276
f_chiral_restr	0.0861
f_bond_d	0.0126
f_plane_restr	0.0122

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5881
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	29

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
XSCALE	data scaling
PHASER	phasing