8HVB

Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, lacto-N-biose complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.3 M Ammonium fluoride, 10%(w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.925	α = 90
b = 51.344	β = 98.03
c = 86.507	γ = 90

Symmetry
Space Group	P 1 21 1

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 4M		2022-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.052000	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.6	48.5	100	0.142	0.153	0.057	0.994	9.1	7		62063			12.18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	100		0.973	1.049	0.391	0.913	3.1	7.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.6	48.5	58988	3060	99.99	0.1509	0.14918	0.18406	RANDOM	15.474

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]
0.08		0.61	0.69		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.579
r_dihedral_angle_2_deg	7.735
r_dihedral_angle_1_deg	6.831
r_long_range_B_refined	4.622
r_long_range_B_other	4.622
r_scangle_other	3.796
r_scbond_it	2.458
r_scbond_other	2.458
r_mcangle_other	2.236
r_mcangle_it	2.235
r_angle_refined_deg	1.585
r_mcbond_it	1.504
r_mcbond_other	1.502
r_angle_other_deg	0.542
r_chiral_restr	0.08
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4593
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing