6LI7

Crystal Structure of Lectin from Pleurotus ostreatus in complex with GalNAc

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3W5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	300	0.9M Na2HPO4/K2HPO4, pH 5.5, 33% glycerol

Crystal Properties
Matthews coefficient	Solvent content
6.26	80.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.273	α = 90
b = 152.273	β = 90
c = 145.975	γ = 120

Symmetry
Space Group	P 61 2 2

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 X 16M	Si 111. Rosenbaum-Rock double-crystal monochromator	2018-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.99	APS	22-ID

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	2.098	30	99.9	0.996	16.3	5		58637

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	2.1	2.18			0.996

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3W5N	2.098	29.642	58628	2000	99.899	0.193	0.1927	0.2055	32.103

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]
0.006	0.003		0.006		-0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.148
r_dihedral_angle_4_deg	22.108
r_dihedral_angle_3_deg	12.688
r_dihedral_angle_1_deg	10.495
r_lrange_it	7.483
r_lrange_other	7.307
r_scangle_it	6.244
r_scangle_other	6.242
r_scbond_it	4.601
r_scbond_other	4.6
r_mcangle_it	3.861
r_mcangle_other	3.86
r_mcbond_it	2.922
r_mcbond_other	2.921
r_angle_refined_deg	2.098
r_angle_other_deg	1.469
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.177
r_nbd_other	0.144
r_symmetry_xyhbond_nbd_other	0.101
r_metal_ion_refined	0.1
r_symmetry_nbtor_other	0.098
r_chiral_restr	0.089
r_symmetry_nbd_refined	0.069
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2505
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	113

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
BALBES	phasing