6V7G | pdb_00006v7g

Binding of Benzoic Acid and Anions Within the Cupin Domains of the Vicillin Protein Canavalin from Jack Bean (canavalia ensiformis): Crystal Structures

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CB4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	Vapor diffusion in sitting drop Cryschem plates. Reservoirs were 1.0 M sodium citrate titrated with acetic acid to pH6.0. Drops were initially equal amounts of the reservoir solution with a protein stock solution of 30 mg/ml canavalin in water with a trace of ammonium hydroxide. At room temperature crystallization time was about three weeks.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.806	α = 90
b = 125.806	β = 90
c = 49.875	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	PIXEL	DECTRIS PILATUS3 R CdTe 300K		2018-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0	ALS	8.3.1

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)	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	1.4	109	99.6	0.258	0.248	0.26	0.029	0.99	18.7	61		86853			14.6

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	1.4	1.43	92.8		0.182	0.7	11.8

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 (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	6CB4	1.4	109	84484	4348	99.99	0.1614	0.1601	0.17	0.188	0.19	RANDOM	28.707

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]
-0.66	-0.33		-0.66		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.2
r_dihedral_angle_4_deg	23.813
r_dihedral_angle_3_deg	13.794
r_dihedral_angle_1_deg	6.611
r_angle_refined_deg	1.579
r_angle_other_deg	1.427
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.2
r_dihedral_angle_4_deg	23.813
r_dihedral_angle_3_deg	13.794
r_dihedral_angle_1_deg	6.611
r_angle_refined_deg	1.579
r_angle_other_deg	1.427
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2873
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	39

Software

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

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.