7BBC | pdb_00007bbc

Joint X-ray/neutron room temperature structure of perdeuterated PLL lectin in complex with perdeuterated L-fucose

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5C9O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Na/K tartrate dissolved in D2O, soaked with 50 mM perdeuterated fucose-d12 dissolved in D2O

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.665	α = 90
b = 89.21	β = 90
c = 159.235	γ = 90

Symmetry
Space Group	I 2 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	293	IMAGE PLATE	MAR scanner 345 mm plate		2020-01-15	M	SINGLE WAVELENGTH
2	1	neutron	293	IMAGE PLATE	LADI III		2019-08-04	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	Xenocs GeniX 3D Cu HF	1.542
2	NUCLEAR REACTOR	ILL BEAMLINE LADI III	3.07-4.05	ILL	LADI III

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.84	33	100	0.11				1		14.7	11.5		45276			19.08
2	2.2	46	84.9	0.16						8	4.1		22348			19.08

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.88		0.58				0.83
2	2.2	2.32		0.33

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.84	33		1.37		45271	2265	99.97		0.1222	0.1213	0.12	0.1398	0.14		34.65
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.2	45.99				22233	1112	83.26			0.1906		0.2211			34.65

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	13.9607
f_dihedral_angle_d	13.9607
f_angle_d	1.3225
f_angle_d	1.3225
f_chiral_restr	0.0743
f_chiral_restr	0.0743
f_bond_d	0.0103
f_bond_d	0.0103
f_plane_restr	0.0072
f_plane_restr	0.0072

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2750
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	66

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data processing
Aimless	data scaling
SCALA	data scaling
PHENIX	phasing
LAUEGEN	data processing
LAUEGEN	data reduction
LSCALE	data scaling

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.