3PHZ | pdb_00003phz

Crystal Structure Analysis of Polyporus squamosus lectin bound to human-type influenza-binding epitope Neu5Aca2-6Galb1-4GlcNAc

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IHO	PDB entry 2IHO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	7	293	PEG 8000, pH 7, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.809	α = 90
b = 59.4	β = 90
c = 103.228	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 210				SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.7	38.5	99	0.06	26.3	5.8	79179	78403	2	2	28.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	92.8		0.238	2.68

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2IHO	1.7	38.5	79179	78403	3939	99.02	0.1867	0.1851	0.19	0.217	0.22	RANDOM	28.8929

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
r_dihedral_angle_2_deg	34.943
r_dihedral_angle_4_deg	23.103
r_dihedral_angle_3_deg	12.441
r_dihedral_angle_1_deg	7.396
r_scangle_it	4.558
r_scbond_it	3.032
r_mcangle_it	2.349
r_angle_refined_deg	1.981
r_mcbond_it	1.388
r_chiral_restr	0.151

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.943
r_dihedral_angle_4_deg	23.103
r_dihedral_angle_3_deg	12.441
r_dihedral_angle_1_deg	7.396
r_scangle_it	4.558
r_scbond_it	3.032
r_mcangle_it	2.349
r_angle_refined_deg	1.981
r_mcbond_it	1.388
r_chiral_restr	0.151
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4318
Nucleic Acid Atoms
Solvent Atoms	632
Heterogen Atoms	92

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.